Mon 24 Dec 00:50:03 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 2f4p-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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/2f4p-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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 ============================================================ Mon 24 Dec 00:50:07 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/2f4p-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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 411 and 0 Target number of residues in the AU: 411 Target solvent content: 0.6032 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.2-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.60 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: 21.543 3.200 Wilson plot Bfac: 53.61 9033 reflections ( 99.64 % complete ) and 0 restraints for refining 5212 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3205 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3281 (Rfree = 0.000) for 5212 atoms. Found 46 (46 requested) and removed 65 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.44 Search for helices and strands: 0 residues in 0 chains, 5270 seeds are put forward NCS extension: 0 residues added, 5270 seeds are put forward Round 1: 241 peptides, 49 chains. Longest chain 9 peptides. Score 0.312 Round 2: 318 peptides, 49 chains. Longest chain 16 peptides. Score 0.522 Round 3: 349 peptides, 48 chains. Longest chain 20 peptides. Score 0.601 Round 4: 363 peptides, 49 chains. Longest chain 17 peptides. Score 0.620 Round 5: 356 peptides, 49 chains. Longest chain 20 peptides. Score 0.606 Taking the results from Round 4 Chains 49, Residues 314, Estimated correctness of the model 46.3 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9486 restraints for refining 4294 atoms. 8220 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2845 (Rfree = 0.000) for 4294 atoms. Found 33 (38 requested) and removed 56 (19 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 4214 atoms. Found 32 (38 requested) and removed 39 (19 requested) atoms. Cycle 3: After refmac, R = 0.2601 (Rfree = 0.000) for 4160 atoms. Found 25 (37 requested) and removed 29 (18 requested) atoms. Cycle 4: After refmac, R = 0.2439 (Rfree = 0.000) for 4125 atoms. Found 23 (37 requested) and removed 28 (18 requested) atoms. Cycle 5: After refmac, R = 0.2083 (Rfree = 0.000) for 4103 atoms. Found 11 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 4227 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 4237 seeds are put forward Round 1: 279 peptides, 48 chains. Longest chain 12 peptides. Score 0.433 Round 2: 334 peptides, 49 chains. Longest chain 15 peptides. Score 0.559 Round 3: 315 peptides, 38 chains. Longest chain 17 peptides. Score 0.623 Round 4: 327 peptides, 46 chains. Longest chain 15 peptides. Score 0.573 Round 5: 319 peptides, 42 chains. Longest chain 17 peptides. Score 0.594 Taking the results from Round 3 Chains 40, Residues 277, Estimated correctness of the model 47.1 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9204 restraints for refining 4144 atoms. 8072 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2335 (Rfree = 0.000) for 4144 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 7: After refmac, R = 0.2127 (Rfree = 0.000) for 4112 atoms. Found 9 (37 requested) and removed 25 (18 requested) atoms. Cycle 8: After refmac, R = 0.2012 (Rfree = 0.000) for 4090 atoms. Found 11 (36 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.1979 (Rfree = 0.000) for 4074 atoms. Found 6 (36 requested) and removed 24 (18 requested) atoms. Cycle 10: After refmac, R = 0.1909 (Rfree = 0.000) for 4048 atoms. Found 8 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 4159 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4174 seeds are put forward Round 1: 283 peptides, 41 chains. Longest chain 14 peptides. Score 0.522 Round 2: 324 peptides, 39 chains. Longest chain 22 peptides. Score 0.632 Round 3: 315 peptides, 42 chains. Longest chain 22 peptides. Score 0.585 Round 4: 326 peptides, 42 chains. Longest chain 15 peptides. Score 0.609 Round 5: 336 peptides, 43 chains. Longest chain 19 peptides. Score 0.620 Taking the results from Round 2 Chains 41, Residues 285, Estimated correctness of the model 49.4 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 8946 restraints for refining 4182 atoms. 7705 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2184 (Rfree = 0.000) for 4182 atoms. Found 29 (37 requested) and removed 36 (18 requested) atoms. Cycle 12: After refmac, R = 0.2013 (Rfree = 0.000) for 4163 atoms. Found 11 (37 requested) and removed 27 (18 requested) atoms. Cycle 13: After refmac, R = 0.2025 (Rfree = 0.000) for 4137 atoms. Found 20 (37 requested) and removed 22 (18 requested) atoms. Cycle 14: After refmac, R = 0.1902 (Rfree = 0.000) for 4122 atoms. Found 18 (37 requested) and removed 23 (18 requested) atoms. Cycle 15: After refmac, R = 0.1783 (Rfree = 0.000) for 4111 atoms. Found 8 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4205 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 4231 seeds are put forward Round 1: 286 peptides, 47 chains. Longest chain 12 peptides. Score 0.463 Round 2: 330 peptides, 43 chains. Longest chain 22 peptides. Score 0.608 Round 3: 339 peptides, 40 chains. Longest chain 22 peptides. Score 0.652 Round 4: 336 peptides, 40 chains. Longest chain 25 peptides. Score 0.646 Round 5: 351 peptides, 43 chains. Longest chain 27 peptides. Score 0.649 Taking the results from Round 3 Chains 41, Residues 299, Estimated correctness of the model 54.3 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9239 restraints for refining 4247 atoms. 8019 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2134 (Rfree = 0.000) for 4247 atoms. Found 24 (38 requested) and removed 39 (19 requested) atoms. Cycle 17: After refmac, R = 0.1878 (Rfree = 0.000) for 4226 atoms. Found 10 (37 requested) and removed 26 (18 requested) atoms. Cycle 18: After refmac, R = 0.1798 (Rfree = 0.000) for 4203 atoms. Found 7 (37 requested) and removed 21 (18 requested) atoms. Cycle 19: After refmac, R = 0.1776 (Rfree = 0.000) for 4184 atoms. Found 8 (37 requested) and removed 18 (18 requested) atoms. Cycle 20: After refmac, R = 0.1716 (Rfree = 0.000) for 4173 atoms. Found 4 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 3.34 Search for helices and strands: 0 residues in 0 chains, 4238 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 4259 seeds are put forward Round 1: 317 peptides, 51 chains. Longest chain 18 peptides. Score 0.498 Round 2: 331 peptides, 41 chains. Longest chain 21 peptides. Score 0.628 Round 3: 312 peptides, 41 chains. Longest chain 21 peptides. Score 0.588 Round 4: 327 peptides, 37 chains. Longest chain 21 peptides. Score 0.655 Round 5: 335 peptides, 42 chains. Longest chain 22 peptides. Score 0.627 Taking the results from Round 4 Chains 37, Residues 290, Estimated correctness of the model 55.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9461 restraints for refining 4293 atoms. 8293 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2098 (Rfree = 0.000) for 4293 atoms. Found 32 (38 requested) and removed 36 (19 requested) atoms. Cycle 22: After refmac, R = 0.1985 (Rfree = 0.000) for 4279 atoms. Found 17 (38 requested) and removed 26 (19 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 4264 atoms. Found 19 (38 requested) and removed 21 (19 requested) atoms. Cycle 24: After refmac, R = 0.1811 (Rfree = 0.000) for 4258 atoms. Found 12 (38 requested) and removed 23 (19 requested) atoms. Cycle 25: After refmac, R = 0.1819 (Rfree = 0.000) for 4245 atoms. Found 13 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4343 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4368 seeds are put forward Round 1: 254 peptides, 43 chains. Longest chain 16 peptides. Score 0.424 Round 2: 291 peptides, 45 chains. Longest chain 16 peptides. Score 0.498 Round 3: 298 peptides, 38 chains. Longest chain 22 peptides. Score 0.587 Round 4: 296 peptides, 40 chains. Longest chain 18 peptides. Score 0.563 Round 5: 295 peptides, 37 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 5 Chains 37, Residues 258, Estimated correctness of the model 38.6 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9616 restraints for refining 4294 atoms. 8594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1975 (Rfree = 0.000) for 4294 atoms. Found 28 (38 requested) and removed 26 (19 requested) atoms. Cycle 27: After refmac, R = 0.1780 (Rfree = 0.000) for 4290 atoms. Found 14 (38 requested) and removed 19 (19 requested) atoms. Cycle 28: After refmac, R = 0.1687 (Rfree = 0.000) for 4274 atoms. Found 15 (38 requested) and removed 21 (19 requested) atoms. Cycle 29: After refmac, R = 0.1622 (Rfree = 0.000) for 4266 atoms. Found 11 (38 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.1605 (Rfree = 0.000) for 4256 atoms. Found 12 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 4365 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 4377 seeds are put forward Round 1: 272 peptides, 47 chains. Longest chain 23 peptides. Score 0.426 Round 2: 312 peptides, 47 chains. Longest chain 17 peptides. Score 0.528 Round 3: 287 peptides, 41 chains. Longest chain 24 peptides. Score 0.531 Round 4: 300 peptides, 41 chains. Longest chain 17 peptides. Score 0.562 Round 5: 306 peptides, 39 chains. Longest chain 17 peptides. Score 0.595 Taking the results from Round 5 Chains 39, Residues 267, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9634 restraints for refining 4294 atoms. 8605 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1926 (Rfree = 0.000) for 4294 atoms. Found 35 (38 requested) and removed 23 (19 requested) atoms. Cycle 32: After refmac, R = 0.1760 (Rfree = 0.000) for 4300 atoms. Found 21 (38 requested) and removed 22 (19 requested) atoms. Cycle 33: After refmac, R = 0.1649 (Rfree = 0.000) for 4297 atoms. Found 18 (38 requested) and removed 22 (19 requested) atoms. Cycle 34: After refmac, R = 0.1552 (Rfree = 0.000) for 4291 atoms. Found 9 (38 requested) and removed 22 (19 requested) atoms. Cycle 35: After refmac, R = 0.1551 (Rfree = 0.000) for 4277 atoms. Found 10 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.33 Search for helices and strands: 0 residues in 0 chains, 4387 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 4398 seeds are put forward Round 1: 269 peptides, 48 chains. Longest chain 15 peptides. Score 0.406 Round 2: 302 peptides, 43 chains. Longest chain 16 peptides. Score 0.546 Round 3: 300 peptides, 43 chains. Longest chain 22 peptides. Score 0.541 Round 4: 321 peptides, 40 chains. Longest chain 28 peptides. Score 0.617 Round 5: 301 peptides, 46 chains. Longest chain 21 peptides. Score 0.512 Taking the results from Round 4 Chains 41, Residues 281, Estimated correctness of the model 45.6 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9346 restraints for refining 4294 atoms. 8192 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1984 (Rfree = 0.000) for 4294 atoms. Found 34 (38 requested) and removed 23 (19 requested) atoms. Cycle 37: After refmac, R = 0.1842 (Rfree = 0.000) for 4298 atoms. Found 21 (38 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.1817 (Rfree = 0.000) for 4294 atoms. Found 11 (38 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.1771 (Rfree = 0.000) for 4284 atoms. Found 6 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.2180 (Rfree = 0.000) for 4264 atoms. Found 38 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 3.26 Search for helices and strands: 0 residues in 0 chains, 4373 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 4413 seeds are put forward Round 1: 249 peptides, 47 chains. Longest chain 15 peptides. Score 0.361 Round 2: 293 peptides, 45 chains. Longest chain 16 peptides. Score 0.503 Round 3: 286 peptides, 42 chains. Longest chain 16 peptides. Score 0.518 Round 4: 280 peptides, 43 chains. Longest chain 15 peptides. Score 0.493 Round 5: 287 peptides, 43 chains. Longest chain 16 peptides. Score 0.510 Taking the results from Round 3 Chains 42, Residues 244, Estimated correctness of the model 17.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9732 restraints for refining 4294 atoms. 8798 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1900 (Rfree = 0.000) for 4294 atoms. Found 27 (38 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.1762 (Rfree = 0.000) for 4296 atoms. Found 12 (38 requested) and removed 20 (19 requested) atoms. Cycle 43: After refmac, R = 0.1753 (Rfree = 0.000) for 4285 atoms. Found 9 (38 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.1884 (Rfree = 0.000) for 4267 atoms. Found 29 (38 requested) and removed 25 (19 requested) atoms. Cycle 45: After refmac, R = 0.1731 (Rfree = 0.000) for 4269 atoms. Found 18 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4348 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4368 seeds are put forward Round 1: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.395 Round 2: 251 peptides, 38 chains. Longest chain 15 peptides. Score 0.474 Round 3: 257 peptides, 38 chains. Longest chain 17 peptides. Score 0.490 Round 4: 242 peptides, 39 chains. Longest chain 12 peptides. Score 0.438 Round 5: 262 peptides, 37 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 225, Estimated correctness of the model 15.8 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9033 reflections ( 99.64 % complete ) and 9591 restraints for refining 4294 atoms. 8686 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1915 (Rfree = 0.000) for 4294 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1937 (Rfree = 0.000) for 4272 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 4248 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1736 (Rfree = 0.000) for 4226 atoms. TimeTaking 48.7