null Mon 24 Dec 08:01:25 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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 08:01:29 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.6-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 385 and 0 Target number of residues in the AU: 385 Target solvent content: 0.6283 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 65.52 6336 reflections ( 99.48 % complete ) and 0 restraints for refining 5216 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3411 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2993 (Rfree = 0.000) for 5216 atoms. Found 33 (33 requested) and removed 85 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 5237 seeds are put forward NCS extension: 0 residues added, 5237 seeds are put forward Round 1: 193 peptides, 39 chains. Longest chain 9 peptides. Score 0.293 Round 2: 246 peptides, 43 chains. Longest chain 14 peptides. Score 0.401 Round 3: 272 peptides, 46 chains. Longest chain 13 peptides. Score 0.438 Round 4: 277 peptides, 43 chains. Longest chain 15 peptides. Score 0.485 Round 5: 298 peptides, 48 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 4 Chains 43, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 10082 restraints for refining 4260 atoms. 9189 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2381 (Rfree = 0.000) for 4260 atoms. Found 17 (27 requested) and removed 35 (13 requested) atoms. Cycle 2: After refmac, R = 0.2154 (Rfree = 0.000) for 4172 atoms. Found 17 (27 requested) and removed 26 (13 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 4126 atoms. Found 14 (26 requested) and removed 20 (13 requested) atoms. Cycle 4: After refmac, R = 0.2089 (Rfree = 0.000) for 4115 atoms. Found 5 (26 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.2056 (Rfree = 0.000) for 4089 atoms. Found 2 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.72 Search for helices and strands: 0 residues in 0 chains, 4183 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 4204 seeds are put forward Round 1: 231 peptides, 45 chains. Longest chain 15 peptides. Score 0.332 Round 2: 259 peptides, 41 chains. Longest chain 13 peptides. Score 0.461 Round 3: 260 peptides, 43 chains. Longest chain 12 peptides. Score 0.440 Round 4: 272 peptides, 41 chains. Longest chain 18 peptides. Score 0.494 Round 5: 269 peptides, 39 chains. Longest chain 14 peptides. Score 0.509 Taking the results from Round 5 Chains 39, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9797 restraints for refining 4172 atoms. 8916 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2320 (Rfree = 0.000) for 4172 atoms. Found 19 (26 requested) and removed 49 (13 requested) atoms. Cycle 7: After refmac, R = 0.2119 (Rfree = 0.000) for 4095 atoms. Found 17 (26 requested) and removed 35 (13 requested) atoms. Cycle 8: After refmac, R = 0.2004 (Rfree = 0.000) for 4052 atoms. Found 14 (26 requested) and removed 26 (13 requested) atoms. Cycle 9: After refmac, R = 0.1899 (Rfree = 0.000) for 4028 atoms. Found 13 (25 requested) and removed 24 (12 requested) atoms. Cycle 10: After refmac, R = 0.1812 (Rfree = 0.000) for 4005 atoms. Found 5 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.66 Search for helices and strands: 0 residues in 0 chains, 4125 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4141 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 10 peptides. Score 0.336 Round 2: 267 peptides, 47 chains. Longest chain 11 peptides. Score 0.412 Round 3: 292 peptides, 46 chains. Longest chain 17 peptides. Score 0.490 Round 4: 300 peptides, 44 chains. Longest chain 15 peptides. Score 0.531 Round 5: 290 peptides, 46 chains. Longest chain 12 peptides. Score 0.485 Taking the results from Round 4 Chains 44, Residues 256, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9276 restraints for refining 4130 atoms. 8281 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2071 (Rfree = 0.000) for 4130 atoms. Found 19 (26 requested) and removed 38 (13 requested) atoms. Cycle 12: After refmac, R = 0.1861 (Rfree = 0.000) for 4091 atoms. Found 12 (26 requested) and removed 28 (13 requested) atoms. Cycle 13: After refmac, R = 0.1848 (Rfree = 0.000) for 4064 atoms. Found 5 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.1697 (Rfree = 0.000) for 4035 atoms. Found 4 (25 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.1656 (Rfree = 0.000) for 4018 atoms. Found 5 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 4147 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4161 seeds are put forward Round 1: 214 peptides, 39 chains. Longest chain 14 peptides. Score 0.358 Round 2: 265 peptides, 45 chains. Longest chain 12 peptides. Score 0.430 Round 3: 268 peptides, 46 chains. Longest chain 11 peptides. Score 0.427 Round 4: 268 peptides, 42 chains. Longest chain 15 peptides. Score 0.473 Round 5: 283 peptides, 43 chains. Longest chain 15 peptides. Score 0.500 Taking the results from Round 5 Chains 43, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9680 restraints for refining 4184 atoms. 8763 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2018 (Rfree = 0.000) for 4184 atoms. Found 21 (26 requested) and removed 38 (13 requested) atoms. Cycle 17: After refmac, R = 0.1805 (Rfree = 0.000) for 4148 atoms. Found 13 (26 requested) and removed 24 (13 requested) atoms. Cycle 18: After refmac, R = 0.1657 (Rfree = 0.000) for 4126 atoms. Found 7 (26 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.1620 (Rfree = 0.000) for 4112 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.1587 (Rfree = 0.000) for 4095 atoms. Found 3 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.71 Search for helices and strands: 0 residues in 0 chains, 4160 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4184 seeds are put forward Round 1: 205 peptides, 38 chains. Longest chain 12 peptides. Score 0.344 Round 2: 249 peptides, 40 chains. Longest chain 14 peptides. Score 0.446 Round 3: 268 peptides, 40 chains. Longest chain 15 peptides. Score 0.495 Round 4: 275 peptides, 38 chains. Longest chain 16 peptides. Score 0.535 Round 5: 253 peptides, 32 chains. Longest chain 23 peptides. Score 0.546 Taking the results from Round 5 Chains 32, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9952 restraints for refining 4247 atoms. 9100 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1918 (Rfree = 0.000) for 4247 atoms. Found 16 (27 requested) and removed 37 (13 requested) atoms. Cycle 22: After refmac, R = 0.1726 (Rfree = 0.000) for 4219 atoms. Found 9 (27 requested) and removed 19 (13 requested) atoms. Cycle 23: After refmac, R = 0.1674 (Rfree = 0.000) for 4199 atoms. Found 6 (26 requested) and removed 19 (13 requested) atoms. Cycle 24: After refmac, R = 0.1636 (Rfree = 0.000) for 4182 atoms. Found 10 (26 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.1564 (Rfree = 0.000) for 4175 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.67 Search for helices and strands: 0 residues in 0 chains, 4270 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 4307 seeds are put forward Round 1: 223 peptides, 41 chains. Longest chain 13 peptides. Score 0.359 Round 2: 235 peptides, 36 chains. Longest chain 17 peptides. Score 0.455 Round 3: 234 peptides, 34 chains. Longest chain 17 peptides. Score 0.476 Round 4: 247 peptides, 40 chains. Longest chain 18 peptides. Score 0.440 Round 5: 268 peptides, 35 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 5 Chains 35, Residues 233, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9733 restraints for refining 4264 atoms. 8799 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1928 (Rfree = 0.000) for 4264 atoms. Found 22 (27 requested) and removed 33 (13 requested) atoms. Cycle 27: After refmac, R = 0.1784 (Rfree = 0.000) for 4245 atoms. Found 7 (27 requested) and removed 18 (13 requested) atoms. Cycle 28: After refmac, R = 0.1736 (Rfree = 0.000) for 4232 atoms. Found 2 (27 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.1674 (Rfree = 0.000) for 4217 atoms. Found 8 (27 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.1624 (Rfree = 0.000) for 4208 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 4300 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 4329 seeds are put forward Round 1: 202 peptides, 40 chains. Longest chain 11 peptides. Score 0.308 Round 2: 222 peptides, 37 chains. Longest chain 14 peptides. Score 0.407 Round 3: 245 peptides, 37 chains. Longest chain 19 peptides. Score 0.470 Round 4: 251 peptides, 37 chains. Longest chain 15 peptides. Score 0.486 Round 5: 252 peptides, 37 chains. Longest chain 25 peptides. Score 0.488 Taking the results from Round 5 Chains 39, Residues 215, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9833 restraints for refining 4264 atoms. 8950 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1930 (Rfree = 0.000) for 4264 atoms. Found 19 (27 requested) and removed 24 (13 requested) atoms. Cycle 32: After refmac, R = 0.1787 (Rfree = 0.000) for 4249 atoms. Found 10 (27 requested) and removed 18 (13 requested) atoms. Cycle 33: After refmac, R = 0.1671 (Rfree = 0.000) for 4238 atoms. Found 5 (27 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1617 (Rfree = 0.000) for 4229 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1590 (Rfree = 0.000) for 4216 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.64 Search for helices and strands: 0 residues in 0 chains, 4299 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4316 seeds are put forward Round 1: 203 peptides, 41 chains. Longest chain 9 peptides. Score 0.298 Round 2: 213 peptides, 37 chains. Longest chain 21 peptides. Score 0.381 Round 3: 214 peptides, 36 chains. Longest chain 15 peptides. Score 0.396 Round 4: 216 peptides, 35 chains. Longest chain 14 peptides. Score 0.414 Round 5: 211 peptides, 33 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Chains 33, Residues 178, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 10324 restraints for refining 4263 atoms. 9614 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1836 (Rfree = 0.000) for 4263 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 37: After refmac, R = 0.1693 (Rfree = 0.000) for 4252 atoms. Found 3 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.1642 (Rfree = 0.000) for 4225 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.1635 (Rfree = 0.000) for 4212 atoms. Found 13 (27 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1561 (Rfree = 0.000) for 4210 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 4283 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4303 seeds are put forward Round 1: 177 peptides, 36 chains. Longest chain 11 peptides. Score 0.282 Round 2: 200 peptides, 35 chains. Longest chain 12 peptides. Score 0.368 Round 3: 204 peptides, 33 chains. Longest chain 13 peptides. Score 0.405 Round 4: 212 peptides, 34 chains. Longest chain 17 peptides. Score 0.416 Round 5: 209 peptides, 34 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 4 Chains 35, Residues 178, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6336 reflections ( 99.48 % complete ) and 9975 restraints for refining 4262 atoms. 9228 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1873 (Rfree = 0.000) for 4262 atoms. Found 26 (27 requested) and removed 23 (13 requested) atoms. Cycle 42: After refmac, R = 0.1650 (Rfree = 0.000) for 4253 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 43: After refmac, R = 0.1604 (Rfree = 0.000) for 4238 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 44: After refmac, R = 0.1563 (Rfree = 0.000) for 4224 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.1550 (Rfree = 0.000) for 4213 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.69 Search for helices and strands: 0 residues in 0 chains, 4291 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 4313 seeds are put forward Round 1: 195 peptides, 38 chains. Longest chain 9 peptides. Score 0.312 Round 2: 231 peptides, 39 chains. Longest chain 13 peptides. Score 0.408 Round 3: 232 peptides, 39 chains. Longest chain 14 peptides. Score 0.410 Round 4: 237 peptides, 37 chains. Longest chain 13 peptides. Score 0.449 Round 5: 230 peptides, 39 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 200, 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. 6336 reflections ( 99.48 % complete ) and 10192 restraints for refining 4264 atoms. 9429 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1929 (Rfree = 0.000) for 4264 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1781 (Rfree = 0.000) for 4244 atoms. Found 0 (27 requested) and removed 11 (13 requested) atoms. Cycle 48: After refmac, R = 0.1709 (Rfree = 0.000) for 4227 atoms. Found 0 (27 requested) and removed 11 (13 requested) atoms. Cycle 49: After refmac, R = 0.1704 (Rfree = 0.000) for 4215 atoms. Found 0 (27 requested) and removed 1 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:51:19 GMT 2018 Job finished. TimeTaking 49.9 Used memory is bytes: 5050584