Mon 24 Dec 07:56:09 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 2f4p-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-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/2f4p-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-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 07:56:13 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/2f4p-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6176 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-3.4-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 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 3.400 Wilson plot Bfac: 59.95 7529 reflections ( 99.56 % complete ) and 0 restraints for refining 5176 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3417 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3468 (Rfree = 0.000) for 5176 atoms. Found 39 (39 requested) and removed 97 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.60 Search for helices and strands: 0 residues in 0 chains, 5187 seeds are put forward NCS extension: 0 residues added, 5187 seeds are put forward Round 1: 200 peptides, 41 chains. Longest chain 10 peptides. Score 0.288 Round 2: 270 peptides, 46 chains. Longest chain 15 peptides. Score 0.432 Round 3: 279 peptides, 51 chains. Longest chain 12 peptides. Score 0.398 Round 4: 292 peptides, 48 chains. Longest chain 12 peptides. Score 0.468 Round 5: 301 peptides, 52 chains. Longest chain 16 peptides. Score 0.447 Taking the results from Round 4 Chains 48, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9929 restraints for refining 4275 atoms. 9001 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2941 (Rfree = 0.000) for 4275 atoms. Found 29 (32 requested) and removed 73 (16 requested) atoms. Cycle 2: After refmac, R = 0.2744 (Rfree = 0.000) for 4140 atoms. Found 25 (31 requested) and removed 46 (15 requested) atoms. Cycle 3: After refmac, R = 0.2583 (Rfree = 0.000) for 4070 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 4: After refmac, R = 0.2500 (Rfree = 0.000) for 4038 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 5: After refmac, R = 0.2568 (Rfree = 0.000) for 4010 atoms. Found 20 (30 requested) and removed 34 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.61 Search for helices and strands: 0 residues in 0 chains, 4141 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4157 seeds are put forward Round 1: 242 peptides, 50 chains. Longest chain 9 peptides. Score 0.302 Round 2: 271 peptides, 49 chains. Longest chain 11 peptides. Score 0.400 Round 3: 279 peptides, 48 chains. Longest chain 15 peptides. Score 0.433 Round 4: 296 peptides, 48 chains. Longest chain 16 peptides. Score 0.478 Round 5: 291 peptides, 49 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 4 Chains 48, Residues 248, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9134 restraints for refining 4030 atoms. 8190 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2582 (Rfree = 0.000) for 4030 atoms. Found 30 (30 requested) and removed 51 (15 requested) atoms. Cycle 7: After refmac, R = 0.2836 (Rfree = 0.000) for 3977 atoms. Found 30 (30 requested) and removed 59 (15 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 3916 atoms. Found 20 (29 requested) and removed 24 (14 requested) atoms. Cycle 9: After refmac, R = 0.2140 (Rfree = 0.000) for 3896 atoms. Found 23 (29 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.1979 (Rfree = 0.000) for 3893 atoms. Found 16 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.53 Search for helices and strands: 0 residues in 0 chains, 4043 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4058 seeds are put forward Round 1: 229 peptides, 44 chains. Longest chain 12 peptides. Score 0.339 Round 2: 266 peptides, 50 chains. Longest chain 10 peptides. Score 0.373 Round 3: 296 peptides, 49 chains. Longest chain 14 peptides. Score 0.467 Round 4: 302 peptides, 49 chains. Longest chain 15 peptides. Score 0.482 Round 5: 301 peptides, 48 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 5 Chains 48, Residues 253, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9376 restraints for refining 4193 atoms. 8356 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2614 (Rfree = 0.000) for 4193 atoms. Found 25 (31 requested) and removed 59 (15 requested) atoms. Cycle 12: After refmac, R = 0.2200 (Rfree = 0.000) for 4116 atoms. Found 25 (31 requested) and removed 26 (15 requested) atoms. Cycle 13: After refmac, R = 0.2252 (Rfree = 0.000) for 4099 atoms. Found 21 (31 requested) and removed 32 (15 requested) atoms. Cycle 14: After refmac, R = 0.2090 (Rfree = 0.000) for 4077 atoms. Found 29 (30 requested) and removed 23 (15 requested) atoms. Cycle 15: After refmac, R = 0.2483 (Rfree = 0.000) for 4073 atoms. Found 30 (30 requested) and removed 42 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 4175 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4192 seeds are put forward Round 1: 232 peptides, 49 chains. Longest chain 9 peptides. Score 0.284 Round 2: 280 peptides, 49 chains. Longest chain 15 peptides. Score 0.424 Round 3: 271 peptides, 48 chains. Longest chain 12 peptides. Score 0.411 Round 4: 259 peptides, 43 chains. Longest chain 17 peptides. Score 0.437 Round 5: 265 peptides, 46 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 4 Chains 43, Residues 216, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9658 restraints for refining 4233 atoms. 8822 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2889 (Rfree = 0.000) for 4233 atoms. Found 31 (31 requested) and removed 79 (15 requested) atoms. Cycle 17: After refmac, R = 0.2320 (Rfree = 0.000) for 4139 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 18: After refmac, R = 0.2252 (Rfree = 0.000) for 4122 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 19: After refmac, R = 0.2237 (Rfree = 0.000) for 4118 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 4112 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 4248 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4275 seeds are put forward Round 1: 200 peptides, 43 chains. Longest chain 9 peptides. Score 0.261 Round 2: 245 peptides, 43 chains. Longest chain 12 peptides. Score 0.398 Round 3: 254 peptides, 46 chains. Longest chain 12 peptides. Score 0.388 Round 4: 276 peptides, 48 chains. Longest chain 13 peptides. Score 0.425 Round 5: 255 peptides, 41 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 42, Residues 214, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9776 restraints for refining 4277 atoms. 8912 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2212 (Rfree = 0.000) for 4277 atoms. Found 31 (32 requested) and removed 34 (16 requested) atoms. Cycle 22: After refmac, R = 0.2014 (Rfree = 0.000) for 4242 atoms. Found 23 (32 requested) and removed 22 (16 requested) atoms. Cycle 23: After refmac, R = 0.2338 (Rfree = 0.000) for 4212 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 24: After refmac, R = 0.1787 (Rfree = 0.000) for 4192 atoms. Found 20 (31 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.1849 (Rfree = 0.000) for 4186 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 4267 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4283 seeds are put forward Round 1: 198 peptides, 42 chains. Longest chain 8 peptides. Score 0.268 Round 2: 244 peptides, 44 chains. Longest chain 10 peptides. Score 0.383 Round 3: 257 peptides, 47 chains. Longest chain 10 peptides. Score 0.384 Round 4: 263 peptides, 46 chains. Longest chain 12 peptides. Score 0.413 Round 5: 283 peptides, 47 chains. Longest chain 14 peptides. Score 0.455 Taking the results from Round 5 Chains 47, Residues 236, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9766 restraints for refining 4277 atoms. 8834 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2173 (Rfree = 0.000) for 4277 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 27: After refmac, R = 0.1740 (Rfree = 0.000) for 4257 atoms. Found 23 (32 requested) and removed 23 (16 requested) atoms. Cycle 28: After refmac, R = 0.1753 (Rfree = 0.000) for 4247 atoms. Found 28 (32 requested) and removed 25 (16 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1648 (Rfree = 0.000) for 4238 atoms. Found 29 (32 requested) and removed 21 (16 requested) atoms. Cycle 30: After refmac, R = 0.1639 (Rfree = 0.000) for 4240 atoms. Found 31 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.54 Search for helices and strands: 0 residues in 0 chains, 4371 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4385 seeds are put forward Round 1: 210 peptides, 44 chains. Longest chain 10 peptides. Score 0.280 Round 2: 242 peptides, 44 chains. Longest chain 10 peptides. Score 0.378 Round 3: 269 peptides, 51 chains. Longest chain 11 peptides. Score 0.370 Round 4: 252 peptides, 43 chains. Longest chain 11 peptides. Score 0.418 Round 5: 238 peptides, 38 chains. Longest chain 25 peptides. Score 0.439 Taking the results from Round 5 Chains 39, Residues 200, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9785 restraints for refining 4276 atoms. 8974 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2158 (Rfree = 0.000) for 4276 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 32: After refmac, R = 0.1710 (Rfree = 0.000) for 4269 atoms. Found 22 (32 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.1693 (Rfree = 0.000) for 4263 atoms. Found 24 (32 requested) and removed 23 (16 requested) atoms. Cycle 34: After refmac, R = 0.1404 (Rfree = 0.000) for 4260 atoms. Found 13 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.1463 (Rfree = 0.000) for 4247 atoms. Found 10 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.55 Search for helices and strands: 0 residues in 0 chains, 4368 seeds are put forward NCS extension: 45 residues added (0 deleted due to clashes), 4413 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 11 peptides. Score 0.289 Round 2: 220 peptides, 40 chains. Longest chain 14 peptides. Score 0.363 Round 3: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.368 Round 4: 208 peptides, 36 chains. Longest chain 18 peptides. Score 0.379 Round 5: 219 peptides, 38 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 5 Chains 39, Residues 181, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9839 restraints for refining 4275 atoms. 9083 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1793 (Rfree = 0.000) for 4275 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 37: After refmac, R = 0.1639 (Rfree = 0.000) for 4261 atoms. Found 26 (32 requested) and removed 21 (16 requested) atoms. Cycle 38: After refmac, R = 0.1537 (Rfree = 0.000) for 4251 atoms. Found 19 (32 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.1588 (Rfree = 0.000) for 4245 atoms. Found 20 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1559 (Rfree = 0.000) for 4242 atoms. Found 23 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.56 Search for helices and strands: 0 residues in 0 chains, 4344 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4361 seeds are put forward Round 1: 178 peptides, 40 chains. Longest chain 9 peptides. Score 0.230 Round 2: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.296 Round 3: 231 peptides, 40 chains. Longest chain 15 peptides. Score 0.395 Round 4: 218 peptides, 39 chains. Longest chain 12 peptides. Score 0.370 Round 5: 204 peptides, 37 chains. Longest chain 16 peptides. Score 0.354 Taking the results from Round 3 Chains 40, Residues 191, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9848 restraints for refining 4275 atoms. 9070 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1810 (Rfree = 0.000) for 4275 atoms. Found 27 (32 requested) and removed 19 (16 requested) atoms. Cycle 42: After refmac, R = 0.1661 (Rfree = 0.000) for 4267 atoms. Found 21 (32 requested) and removed 21 (16 requested) atoms. Cycle 43: After refmac, R = 0.1606 (Rfree = 0.000) for 4256 atoms. Found 30 (32 requested) and removed 17 (16 requested) atoms. Cycle 44: After refmac, R = 0.1530 (Rfree = 0.000) for 4264 atoms. Found 18 (32 requested) and removed 20 (16 requested) atoms. Cycle 45: After refmac, R = 0.1508 (Rfree = 0.000) for 4258 atoms. Found 25 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.56 Search for helices and strands: 0 residues in 0 chains, 4369 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4383 seeds are put forward Round 1: 184 peptides, 40 chains. Longest chain 8 peptides. Score 0.250 Round 2: 206 peptides, 37 chains. Longest chain 11 peptides. Score 0.360 Round 3: 207 peptides, 36 chains. Longest chain 13 peptides. Score 0.376 Round 4: 200 peptides, 34 chains. Longest chain 15 peptides. Score 0.381 Round 5: 198 peptides, 36 chains. Longest chain 12 peptides. Score 0.348 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 166, 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 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7529 reflections ( 99.56 % complete ) and 10119 restraints for refining 4277 atoms. 9489 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1711 (Rfree = 0.000) for 4277 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 4257 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1583 (Rfree = 0.000) for 4240 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1531 (Rfree = 0.000) for 4219 atoms. TimeTaking 54.27