null Sun 23 Dec 22:22:49 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 2ffj-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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/2ffj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 22:22:59 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/2ffj-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 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-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: 19 Cell parameters: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.8-parrot-hancs.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 5324 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3441 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3610 (Rfree = 0.000) for 5324 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 5453 seeds are put forward NCS extension: 0 residues added, 5453 seeds are put forward Round 1: 226 peptides, 45 chains. Longest chain 11 peptides. Score 0.298 Round 2: 304 peptides, 47 chains. Longest chain 20 peptides. Score 0.467 Round 3: 312 peptides, 42 chains. Longest chain 21 peptides. Score 0.531 Round 4: 307 peptides, 40 chains. Longest chain 21 peptides. Score 0.539 Round 5: 312 peptides, 41 chains. Longest chain 15 peptides. Score 0.540 Taking the results from Round 5 Chains 41, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9903 restraints for refining 4256 atoms. 8860 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2869 (Rfree = 0.000) for 4256 atoms. Found 16 (23 requested) and removed 46 (11 requested) atoms. Cycle 2: After refmac, R = 0.2661 (Rfree = 0.000) for 4165 atoms. Found 22 (23 requested) and removed 44 (11 requested) atoms. Cycle 3: After refmac, R = 0.2550 (Rfree = 0.000) for 4114 atoms. Found 19 (22 requested) and removed 40 (11 requested) atoms. Cycle 4: After refmac, R = 0.2483 (Rfree = 0.000) for 4071 atoms. Found 19 (22 requested) and removed 40 (11 requested) atoms. Cycle 5: After refmac, R = 0.2407 (Rfree = 0.000) for 4028 atoms. Found 21 (22 requested) and removed 32 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 4223 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4241 seeds are put forward Round 1: 263 peptides, 50 chains. Longest chain 11 peptides. Score 0.339 Round 2: 305 peptides, 43 chains. Longest chain 19 peptides. Score 0.507 Round 3: 300 peptides, 41 chains. Longest chain 13 peptides. Score 0.516 Round 4: 301 peptides, 37 chains. Longest chain 19 peptides. Score 0.554 Round 5: 310 peptides, 40 chains. Longest chain 20 peptides. Score 0.545 Taking the results from Round 4 Chains 37, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9254 restraints for refining 4017 atoms. 8235 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2796 (Rfree = 0.000) for 4017 atoms. Found 16 (22 requested) and removed 49 (11 requested) atoms. Cycle 7: After refmac, R = 0.2474 (Rfree = 0.000) for 3953 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 8: After refmac, R = 0.2393 (Rfree = 0.000) for 3922 atoms. Found 13 (21 requested) and removed 24 (10 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 3896 atoms. Found 17 (21 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.2249 (Rfree = 0.000) for 3882 atoms. Found 17 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4085 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4102 seeds are put forward Round 1: 267 peptides, 48 chains. Longest chain 11 peptides. Score 0.371 Round 2: 305 peptides, 45 chains. Longest chain 15 peptides. Score 0.489 Round 3: 288 peptides, 46 chains. Longest chain 12 peptides. Score 0.441 Round 4: 302 peptides, 45 chains. Longest chain 19 peptides. Score 0.482 Round 5: 294 peptides, 39 chains. Longest chain 23 peptides. Score 0.522 Taking the results from Round 5 Chains 39, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9354 restraints for refining 4080 atoms. 8373 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2564 (Rfree = 0.000) for 4080 atoms. Found 17 (22 requested) and removed 36 (11 requested) atoms. Cycle 12: After refmac, R = 0.2498 (Rfree = 0.000) for 4029 atoms. Found 14 (22 requested) and removed 34 (11 requested) atoms. Cycle 13: After refmac, R = 0.2431 (Rfree = 0.000) for 3984 atoms. Found 20 (22 requested) and removed 22 (11 requested) atoms. Cycle 14: After refmac, R = 0.2256 (Rfree = 0.000) for 3954 atoms. Found 16 (21 requested) and removed 30 (10 requested) atoms. Cycle 15: After refmac, R = 0.1928 (Rfree = 0.000) for 3922 atoms. Found 4 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 4115 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4140 seeds are put forward Round 1: 264 peptides, 50 chains. Longest chain 12 peptides. Score 0.342 Round 2: 307 peptides, 46 chains. Longest chain 25 peptides. Score 0.483 Round 3: 320 peptides, 46 chains. Longest chain 19 peptides. Score 0.511 Round 4: 323 peptides, 43 chains. Longest chain 19 peptides. Score 0.544 Round 5: 318 peptides, 41 chains. Longest chain 28 peptides. Score 0.552 Taking the results from Round 5 Chains 43, Residues 277, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9036 restraints for refining 4207 atoms. 7848 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2444 (Rfree = 0.000) for 4207 atoms. Found 15 (23 requested) and removed 59 (11 requested) atoms. Cycle 17: After refmac, R = 0.2351 (Rfree = 0.000) for 4122 atoms. Found 17 (22 requested) and removed 30 (11 requested) atoms. Cycle 18: After refmac, R = 0.2353 (Rfree = 0.000) for 4081 atoms. Found 18 (22 requested) and removed 25 (11 requested) atoms. Cycle 19: After refmac, R = 0.2231 (Rfree = 0.000) for 4056 atoms. Found 11 (22 requested) and removed 22 (11 requested) atoms. Cycle 20: After refmac, R = 0.1961 (Rfree = 0.000) for 4024 atoms. Found 4 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 4169 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4189 seeds are put forward Round 1: 260 peptides, 48 chains. Longest chain 19 peptides. Score 0.353 Round 2: 299 peptides, 46 chains. Longest chain 18 peptides. Score 0.466 Round 3: 302 peptides, 40 chains. Longest chain 16 peptides. Score 0.529 Round 4: 298 peptides, 44 chains. Longest chain 14 peptides. Score 0.483 Round 5: 318 peptides, 45 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 3 Chains 40, Residues 262, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9223 restraints for refining 4201 atoms. 8131 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2635 (Rfree = 0.000) for 4201 atoms. Found 19 (23 requested) and removed 45 (11 requested) atoms. Cycle 22: After refmac, R = 0.2425 (Rfree = 0.000) for 4152 atoms. Found 18 (22 requested) and removed 32 (11 requested) atoms. Cycle 23: After refmac, R = 0.2289 (Rfree = 0.000) for 4122 atoms. Found 20 (22 requested) and removed 28 (11 requested) atoms. Cycle 24: After refmac, R = 0.2183 (Rfree = 0.000) for 4095 atoms. Found 13 (22 requested) and removed 16 (11 requested) atoms. Cycle 25: After refmac, R = 0.1823 (Rfree = 0.000) for 4080 atoms. Found 5 (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, 4262 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4280 seeds are put forward Round 1: 253 peptides, 47 chains. Longest chain 15 peptides. Score 0.346 Round 2: 264 peptides, 41 chains. Longest chain 19 peptides. Score 0.436 Round 3: 290 peptides, 41 chains. Longest chain 20 peptides. Score 0.495 Round 4: 300 peptides, 43 chains. Longest chain 17 peptides. Score 0.497 Round 5: 308 peptides, 42 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 5 Chains 43, Residues 266, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9447 restraints for refining 4260 atoms. 8395 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2436 (Rfree = 0.000) for 4260 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 27: After refmac, R = 0.2338 (Rfree = 0.000) for 4205 atoms. Found 19 (23 requested) and removed 31 (11 requested) atoms. Cycle 28: After refmac, R = 0.2169 (Rfree = 0.000) for 4173 atoms. Found 22 (23 requested) and removed 27 (11 requested) atoms. Cycle 29: After refmac, R = 0.2117 (Rfree = 0.000) for 4143 atoms. Found 13 (22 requested) and removed 23 (11 requested) atoms. Cycle 30: After refmac, R = 0.1793 (Rfree = 0.000) for 4116 atoms. Found 6 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 4303 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4321 seeds are put forward Round 1: 223 peptides, 46 chains. Longest chain 10 peptides. Score 0.279 Round 2: 236 peptides, 42 chains. Longest chain 12 peptides. Score 0.358 Round 3: 255 peptides, 39 chains. Longest chain 15 peptides. Score 0.436 Round 4: 273 peptides, 46 chains. Longest chain 13 peptides. Score 0.406 Round 5: 273 peptides, 45 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 3 Chains 39, Residues 216, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9798 restraints for refining 4264 atoms. 8929 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2477 (Rfree = 0.000) for 4264 atoms. Found 20 (23 requested) and removed 37 (11 requested) atoms. Cycle 32: After refmac, R = 0.2326 (Rfree = 0.000) for 4225 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 33: After refmac, R = 0.2217 (Rfree = 0.000) for 4201 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 34: After refmac, R = 0.2135 (Rfree = 0.000) for 4184 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 35: After refmac, R = 0.1730 (Rfree = 0.000) for 4174 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4342 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4358 seeds are put forward Round 1: 194 peptides, 42 chains. Longest chain 11 peptides. Score 0.244 Round 2: 232 peptides, 43 chains. Longest chain 14 peptides. Score 0.336 Round 3: 258 peptides, 44 chains. Longest chain 16 peptides. Score 0.391 Round 4: 252 peptides, 43 chains. Longest chain 15 peptides. Score 0.387 Round 5: 259 peptides, 42 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 43, Residues 217, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9969 restraints for refining 4304 atoms. 9108 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2413 (Rfree = 0.000) for 4304 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 37: After refmac, R = 0.2191 (Rfree = 0.000) for 4272 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 4255 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 39: After refmac, R = 0.2089 (Rfree = 0.000) for 4238 atoms. Found 20 (23 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.2008 (Rfree = 0.000) for 4217 atoms. Found 20 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4371 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4388 seeds are put forward Round 1: 175 peptides, 37 chains. Longest chain 9 peptides. Score 0.250 Round 2: 212 peptides, 37 chains. Longest chain 12 peptides. Score 0.352 Round 3: 221 peptides, 39 chains. Longest chain 10 peptides. Score 0.353 Round 4: 230 peptides, 36 chains. Longest chain 13 peptides. Score 0.408 Round 5: 235 peptides, 40 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 4 Chains 37, Residues 194, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9915 restraints for refining 4256 atoms. 9125 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2430 (Rfree = 0.000) for 4256 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 42: After refmac, R = 0.2207 (Rfree = 0.000) for 4222 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 43: After refmac, R = 0.2106 (Rfree = 0.000) for 4201 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 44: After refmac, R = 0.2100 (Rfree = 0.000) for 4190 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 45: After refmac, R = 0.2015 (Rfree = 0.000) for 4188 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 4357 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4369 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 9 peptides. Score 0.253 Round 2: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.352 Round 3: 188 peptides, 32 chains. Longest chain 13 peptides. Score 0.347 Round 4: 189 peptides, 33 chains. Longest chain 13 peptides. Score 0.337 Round 5: 188 peptides, 31 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 157, 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 10259 restraints for refining 4247 atoms. 9662 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2530 (Rfree = 0.000) for 4247 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 4220 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2284 (Rfree = 0.000) for 4197 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2181 (Rfree = 0.000) for 4174 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:44 GMT 2018 Job finished. TimeTaking 61.91 Used memory is bytes: 11894464