Mon 24 Dec 00:01:53 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 2afb-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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/2afb-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 ============================================================ Mon 24 Dec 00:01:58 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/2afb-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6465 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.75 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: 97.203 3.800 Wilson plot Bfac: 75.97 7461 reflections ( 99.35 % complete ) and 0 restraints for refining 6189 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3268 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3267 (Rfree = 0.000) for 6189 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 6333 seeds are put forward NCS extension: 0 residues added, 6333 seeds are put forward Round 1: 238 peptides, 50 chains. Longest chain 10 peptides. Score 0.267 Round 2: 333 peptides, 55 chains. Longest chain 15 peptides. Score 0.436 Round 3: 366 peptides, 52 chains. Longest chain 17 peptides. Score 0.527 Round 4: 384 peptides, 55 chains. Longest chain 17 peptides. Score 0.536 Round 5: 393 peptides, 56 chains. Longest chain 14 peptides. Score 0.544 Taking the results from Round 5 Chains 57, Residues 337, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11607 restraints for refining 5075 atoms. 10263 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2641 (Rfree = 0.000) for 5075 atoms. Found 25 (27 requested) and removed 35 (13 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 4946 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 3: After refmac, R = 0.2121 (Rfree = 0.000) for 4879 atoms. Found 13 (27 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2044 (Rfree = 0.000) for 4824 atoms. Found 6 (26 requested) and removed 19 (13 requested) atoms. Cycle 5: After refmac, R = 0.1998 (Rfree = 0.000) for 4788 atoms. Found 8 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 4993 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5010 seeds are put forward Round 1: 299 peptides, 53 chains. Longest chain 16 peptides. Score 0.382 Round 2: 372 peptides, 52 chains. Longest chain 24 peptides. Score 0.538 Round 3: 371 peptides, 46 chains. Longest chain 27 peptides. Score 0.584 Round 4: 377 peptides, 46 chains. Longest chain 24 peptides. Score 0.594 Round 5: 379 peptides, 49 chains. Longest chain 24 peptides. Score 0.574 Taking the results from Round 4 Chains 50, Residues 331, Estimated correctness of the model 0.0 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 10793 restraints for refining 4925 atoms. 9337 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2398 (Rfree = 0.000) for 4925 atoms. Found 27 (27 requested) and removed 46 (13 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 4872 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 8: After refmac, R = 0.2325 (Rfree = 0.000) for 4829 atoms. Found 23 (26 requested) and removed 24 (13 requested) atoms. Cycle 9: After refmac, R = 0.2150 (Rfree = 0.000) for 4805 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 10: After refmac, R = 0.2358 (Rfree = 0.000) for 4789 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 4997 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 5014 seeds are put forward Round 1: 315 peptides, 54 chains. Longest chain 13 peptides. Score 0.407 Round 2: 350 peptides, 52 chains. Longest chain 15 peptides. Score 0.497 Round 3: 363 peptides, 52 chains. Longest chain 23 peptides. Score 0.522 Round 4: 385 peptides, 57 chains. Longest chain 19 peptides. Score 0.522 Round 5: 385 peptides, 51 chains. Longest chain 19 peptides. Score 0.569 Taking the results from Round 5 Chains 51, Residues 334, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11414 restraints for refining 5079 atoms. 10044 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2565 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 35 (13 requested) atoms. Cycle 12: After refmac, R = 0.2369 (Rfree = 0.000) for 5012 atoms. Found 25 (27 requested) and removed 23 (13 requested) atoms. Cycle 13: After refmac, R = 0.2267 (Rfree = 0.000) for 4982 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2173 (Rfree = 0.000) for 4946 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.2044 (Rfree = 0.000) for 4927 atoms. Found 25 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 5125 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 5141 seeds are put forward Round 1: 305 peptides, 58 chains. Longest chain 11 peptides. Score 0.347 Round 2: 357 peptides, 57 chains. Longest chain 21 peptides. Score 0.468 Round 3: 363 peptides, 53 chains. Longest chain 18 peptides. Score 0.513 Round 4: 355 peptides, 54 chains. Longest chain 18 peptides. Score 0.490 Round 5: 362 peptides, 53 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 3 Chains 54, Residues 310, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11594 restraints for refining 5079 atoms. 10296 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2447 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 5037 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 18: After refmac, R = 0.1795 (Rfree = 0.000) for 5009 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2174 (Rfree = 0.000) for 4984 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2014 (Rfree = 0.000) for 4981 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 5158 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5178 seeds are put forward Round 1: 270 peptides, 52 chains. Longest chain 10 peptides. Score 0.325 Round 2: 341 peptides, 53 chains. Longest chain 18 peptides. Score 0.471 Round 3: 333 peptides, 52 chains. Longest chain 16 peptides. Score 0.463 Round 4: 337 peptides, 52 chains. Longest chain 17 peptides. Score 0.471 Round 5: 352 peptides, 54 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 5 Chains 55, Residues 298, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12050 restraints for refining 5080 atoms. 10877 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2641 (Rfree = 0.000) for 5080 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 22: After refmac, R = 0.2392 (Rfree = 0.000) for 5027 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 23: After refmac, R = 0.2225 (Rfree = 0.000) for 4997 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2119 (Rfree = 0.000) for 4971 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 25: After refmac, R = 0.2021 (Rfree = 0.000) for 4954 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5157 seeds are put forward Round 1: 256 peptides, 51 chains. Longest chain 11 peptides. Score 0.301 Round 2: 308 peptides, 48 chains. Longest chain 14 peptides. Score 0.448 Round 3: 300 peptides, 48 chains. Longest chain 13 peptides. Score 0.431 Round 4: 299 peptides, 48 chains. Longest chain 15 peptides. Score 0.429 Round 5: 316 peptides, 49 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 5 Chains 50, Residues 267, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12295 restraints for refining 5078 atoms. 11229 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2335 (Rfree = 0.000) for 5078 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 27: After refmac, R = 0.2043 (Rfree = 0.000) for 5041 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 28: After refmac, R = 0.2157 (Rfree = 0.000) for 5032 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 29: After refmac, R = 0.2008 (Rfree = 0.000) for 5017 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.1792 (Rfree = 0.000) for 5005 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5236 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 9 peptides. Score 0.270 Round 2: 282 peptides, 49 chains. Longest chain 13 peptides. Score 0.382 Round 3: 288 peptides, 45 chains. Longest chain 15 peptides. Score 0.433 Round 4: 307 peptides, 49 chains. Longest chain 14 peptides. Score 0.437 Round 5: 312 peptides, 49 chains. Longest chain 20 peptides. Score 0.447 Taking the results from Round 5 Chains 50, Residues 263, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 11975 restraints for refining 5079 atoms. 10880 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2418 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 32: After refmac, R = 0.2134 (Rfree = 0.000) for 5042 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 33: After refmac, R = 0.2177 (Rfree = 0.000) for 5013 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 34: After refmac, R = 0.2013 (Rfree = 0.000) for 4989 atoms. Found 27 (27 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.2090 (Rfree = 0.000) for 4982 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 5179 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 5212 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 13 peptides. Score 0.295 Round 2: 278 peptides, 49 chains. Longest chain 10 peptides. Score 0.373 Round 3: 294 peptides, 48 chains. Longest chain 14 peptides. Score 0.418 Round 4: 286 peptides, 50 chains. Longest chain 17 peptides. Score 0.381 Round 5: 280 peptides, 44 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 5 Chains 44, Residues 236, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7461 reflections ( 99.35 % complete ) and 12132 restraints for refining 5079 atoms. 11167 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2346 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 37: After refmac, R = 0.2148 (Rfree = 0.000) for 5026 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.1963 (Rfree = 0.000) for 5022 atoms. Found 19 (27 requested) and removed 22 (13 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1952 (Rfree = 0.000) for 5001 atoms. Found 20 (27 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 4994 atoms. Found 25 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 5163 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 5189 seeds are put forward Round 1: 227 peptides, 50 chains. Longest chain 12 peptides. Score 0.239 Round 2: 264 peptides, 50 chains. Longest chain 12 peptides. Score 0.331 Round 3: 270 peptides, 49 chains. Longest chain 15 peptides. Score 0.355 Round 4: 251 peptides, 39 chains. Longest chain 17 peptides. Score 0.411 Round 5: 282 peptides, 47 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 4 Chains 39, Residues 212, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7461 reflections ( 99.35 % complete ) and 12410 restraints for refining 5079 atoms. 11564 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2077 (Rfree = 0.000) for 5079 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 42: After refmac, R = 0.2150 (Rfree = 0.000) for 5049 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 43: After refmac, R = 0.1950 (Rfree = 0.000) for 5032 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.1518 (Rfree = 0.000) for 5026 atoms. Found 10 (27 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1469 (Rfree = 0.000) for 5013 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 5169 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5191 seeds are put forward Round 1: 198 peptides, 44 chains. Longest chain 8 peptides. Score 0.228 Round 2: 253 peptides, 46 chains. Longest chain 11 peptides. Score 0.345 Round 3: 246 peptides, 41 chains. Longest chain 19 peptides. Score 0.380 Round 4: 230 peptides, 38 chains. Longest chain 11 peptides. Score 0.373 Round 5: 228 peptides, 37 chains. Longest chain 14 peptides. Score 0.379 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 205, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 41 chains (205 residues) following loop building 3 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7461 reflections ( 99.35 % complete ) and 11608 restraints for refining 4932 atoms. 10800 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2044 (Rfree = 0.000) for 4932 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1885 (Rfree = 0.000) for 4902 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 4877 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1433 (Rfree = 0.000) for 4855 atoms. TimeTaking 66.25