null Mon 24 Dec 01:05:21 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 1vkh-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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/1vkh-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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 01:05:26 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/1vkh-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.5918 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.4-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: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4368 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: 19.289 3.400 Wilson plot Bfac: 49.34 6884 reflections ( 99.41 % complete ) and 0 restraints for refining 4814 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3171 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2968 (Rfree = 0.000) for 4814 atoms. Found 36 (36 requested) and removed 101 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 4873 seeds are put forward NCS extension: 0 residues added, 4873 seeds are put forward Round 1: 226 peptides, 46 chains. Longest chain 14 peptides. Score 0.316 Round 2: 267 peptides, 46 chains. Longest chain 13 peptides. Score 0.445 Round 3: 276 peptides, 47 chains. Longest chain 12 peptides. Score 0.459 Round 4: 273 peptides, 44 chains. Longest chain 16 peptides. Score 0.487 Round 5: 294 peptides, 41 chains. Longest chain 17 peptides. Score 0.576 Taking the results from Round 5 Chains 41, Residues 253, Estimated correctness of the model 20.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8903 restraints for refining 3969 atoms. 7932 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2316 (Rfree = 0.000) for 3969 atoms. Found 28 (29 requested) and removed 33 (14 requested) atoms. Cycle 2: After refmac, R = 0.2156 (Rfree = 0.000) for 3935 atoms. Found 20 (29 requested) and removed 24 (14 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 3922 atoms. Found 21 (29 requested) and removed 27 (14 requested) atoms. Cycle 4: After refmac, R = 0.2168 (Rfree = 0.000) for 3895 atoms. Found 26 (29 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2010 (Rfree = 0.000) for 3898 atoms. Found 19 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 4066 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4088 seeds are put forward Round 1: 239 peptides, 43 chains. Longest chain 11 peptides. Score 0.399 Round 2: 279 peptides, 41 chains. Longest chain 14 peptides. Score 0.538 Round 3: 297 peptides, 44 chains. Longest chain 22 peptides. Score 0.551 Round 4: 296 peptides, 40 chains. Longest chain 18 peptides. Score 0.592 Round 5: 306 peptides, 39 chains. Longest chain 22 peptides. Score 0.625 Taking the results from Round 5 Chains 39, Residues 267, Estimated correctness of the model 36.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8985 restraints for refining 3971 atoms. 7956 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2338 (Rfree = 0.000) for 3971 atoms. Found 27 (29 requested) and removed 26 (14 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 3957 atoms. Found 10 (29 requested) and removed 25 (14 requested) atoms. Cycle 8: After refmac, R = 0.2013 (Rfree = 0.000) for 3934 atoms. Found 12 (29 requested) and removed 20 (14 requested) atoms. Cycle 9: After refmac, R = 0.2080 (Rfree = 0.000) for 3922 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.1942 (Rfree = 0.000) for 3928 atoms. Found 18 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 4073 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4090 seeds are put forward Round 1: 242 peptides, 43 chains. Longest chain 11 peptides. Score 0.408 Round 2: 289 peptides, 45 chains. Longest chain 12 peptides. Score 0.519 Round 3: 293 peptides, 47 chains. Longest chain 16 peptides. Score 0.506 Round 4: 288 peptides, 42 chains. Longest chain 13 peptides. Score 0.550 Round 5: 283 peptides, 42 chains. Longest chain 18 peptides. Score 0.537 Taking the results from Round 4 Chains 42, Residues 246, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9237 restraints for refining 3971 atoms. 8295 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2137 (Rfree = 0.000) for 3971 atoms. Found 18 (29 requested) and removed 20 (14 requested) atoms. Cycle 12: After refmac, R = 0.2142 (Rfree = 0.000) for 3960 atoms. Found 26 (29 requested) and removed 25 (14 requested) atoms. Cycle 13: After refmac, R = 0.1965 (Rfree = 0.000) for 3954 atoms. Found 14 (29 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.1995 (Rfree = 0.000) for 3951 atoms. Found 25 (29 requested) and removed 16 (14 requested) atoms. Cycle 15: After refmac, R = 0.1991 (Rfree = 0.000) for 3956 atoms. Found 21 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 4088 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 4104 seeds are put forward Round 1: 265 peptides, 50 chains. Longest chain 11 peptides. Score 0.388 Round 2: 279 peptides, 46 chains. Longest chain 16 peptides. Score 0.480 Round 3: 291 peptides, 43 chains. Longest chain 19 peptides. Score 0.547 Round 4: 296 peptides, 45 chains. Longest chain 16 peptides. Score 0.537 Round 5: 304 peptides, 45 chains. Longest chain 16 peptides. Score 0.558 Taking the results from Round 5 Chains 45, Residues 259, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9130 restraints for refining 3971 atoms. 8139 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2292 (Rfree = 0.000) for 3971 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 17: After refmac, R = 0.2146 (Rfree = 0.000) for 3968 atoms. Found 24 (30 requested) and removed 21 (15 requested) atoms. Cycle 18: After refmac, R = 0.2076 (Rfree = 0.000) for 3968 atoms. Found 22 (29 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.2005 (Rfree = 0.000) for 3966 atoms. Found 19 (29 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.1956 (Rfree = 0.000) for 3957 atoms. Found 15 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 4099 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4114 seeds are put forward Round 1: 237 peptides, 43 chains. Longest chain 14 peptides. Score 0.393 Round 2: 265 peptides, 44 chains. Longest chain 15 peptides. Score 0.464 Round 3: 278 peptides, 44 chains. Longest chain 17 peptides. Score 0.501 Round 4: 263 peptides, 40 chains. Longest chain 13 peptides. Score 0.507 Round 5: 268 peptides, 39 chains. Longest chain 12 peptides. Score 0.533 Taking the results from Round 5 Chains 39, Residues 229, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9172 restraints for refining 3971 atoms. 8295 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2034 (Rfree = 0.000) for 3971 atoms. Found 19 (29 requested) and removed 19 (14 requested) atoms. Cycle 22: After refmac, R = 0.1900 (Rfree = 0.000) for 3962 atoms. Found 18 (29 requested) and removed 16 (14 requested) atoms. Cycle 23: After refmac, R = 0.1861 (Rfree = 0.000) for 3956 atoms. Found 17 (29 requested) and removed 18 (14 requested) atoms. Cycle 24: After refmac, R = 0.1901 (Rfree = 0.000) for 3953 atoms. Found 17 (29 requested) and removed 17 (14 requested) atoms. Cycle 25: After refmac, R = 0.1884 (Rfree = 0.000) for 3943 atoms. Found 19 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 4063 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4080 seeds are put forward Round 1: 228 peptides, 43 chains. Longest chain 11 peptides. Score 0.364 Round 2: 246 peptides, 43 chains. Longest chain 12 peptides. Score 0.420 Round 3: 252 peptides, 41 chains. Longest chain 12 peptides. Score 0.464 Round 4: 256 peptides, 42 chains. Longest chain 12 peptides. Score 0.463 Round 5: 252 peptides, 41 chains. Longest chain 13 peptides. Score 0.464 Taking the results from Round 5 Chains 41, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9159 restraints for refining 3971 atoms. 8356 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1982 (Rfree = 0.000) for 3971 atoms. Found 22 (29 requested) and removed 19 (14 requested) atoms. Cycle 27: After refmac, R = 0.1852 (Rfree = 0.000) for 3967 atoms. Found 13 (30 requested) and removed 18 (15 requested) atoms. Cycle 28: After refmac, R = 0.1814 (Rfree = 0.000) for 3959 atoms. Found 9 (29 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.1879 (Rfree = 0.000) for 3945 atoms. Found 17 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.1842 (Rfree = 0.000) for 3943 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 4079 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4092 seeds are put forward Round 1: 228 peptides, 47 chains. Longest chain 9 peptides. Score 0.308 Round 2: 253 peptides, 46 chains. Longest chain 12 peptides. Score 0.403 Round 3: 254 peptides, 43 chains. Longest chain 21 peptides. Score 0.445 Round 4: 252 peptides, 42 chains. Longest chain 14 peptides. Score 0.451 Round 5: 255 peptides, 47 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 42, Residues 210, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9173 restraints for refining 3971 atoms. 8350 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2038 (Rfree = 0.000) for 3971 atoms. Found 22 (29 requested) and removed 18 (14 requested) atoms. Cycle 32: After refmac, R = 0.1914 (Rfree = 0.000) for 3970 atoms. Found 21 (30 requested) and removed 16 (15 requested) atoms. Cycle 33: After refmac, R = 0.1905 (Rfree = 0.000) for 3970 atoms. Found 15 (30 requested) and removed 19 (15 requested) atoms. Cycle 34: After refmac, R = 0.1921 (Rfree = 0.000) for 3960 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1921 (Rfree = 0.000) for 3968 atoms. Found 20 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 4099 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4119 seeds are put forward Round 1: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.292 Round 2: 215 peptides, 37 chains. Longest chain 11 peptides. Score 0.404 Round 3: 236 peptides, 40 chains. Longest chain 12 peptides. Score 0.429 Round 4: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.462 Round 5: 229 peptides, 38 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 4 Chains 37, Residues 197, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9197 restraints for refining 3971 atoms. 8397 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1950 (Rfree = 0.000) for 3971 atoms. Found 14 (29 requested) and removed 20 (14 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 3957 atoms. Found 24 (29 requested) and removed 16 (14 requested) atoms. Cycle 38: After refmac, R = 0.1884 (Rfree = 0.000) for 3958 atoms. Found 27 (29 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1904 (Rfree = 0.000) for 3964 atoms. Found 20 (29 requested) and removed 18 (14 requested) atoms. Cycle 40: After refmac, R = 0.1900 (Rfree = 0.000) for 3962 atoms. Found 21 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 4082 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4098 seeds are put forward Round 1: 190 peptides, 38 chains. Longest chain 10 peptides. Score 0.307 Round 2: 220 peptides, 36 chains. Longest chain 17 peptides. Score 0.433 Round 3: 209 peptides, 33 chains. Longest chain 20 peptides. Score 0.439 Round 4: 210 peptides, 35 chains. Longest chain 13 peptides. Score 0.415 Round 5: 212 peptides, 36 chains. Longest chain 15 peptides. Score 0.408 Taking the results from Round 3 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9423 restraints for refining 3971 atoms. 8752 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1986 (Rfree = 0.000) for 3971 atoms. Found 23 (29 requested) and removed 17 (14 requested) atoms. Cycle 42: After refmac, R = 0.2110 (Rfree = 0.000) for 3976 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 43: After refmac, R = 0.2019 (Rfree = 0.000) for 3978 atoms. Found 30 (30 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.2140 (Rfree = 0.000) for 3988 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 45: After refmac, R = 0.1776 (Rfree = 0.000) for 3991 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 4089 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4112 seeds are put forward Round 1: 169 peptides, 36 chains. Longest chain 8 peptides. Score 0.262 Round 2: 210 peptides, 38 chains. Longest chain 11 peptides. Score 0.374 Round 3: 208 peptides, 32 chains. Longest chain 13 peptides. Score 0.450 Round 4: 192 peptides, 31 chains. Longest chain 12 peptides. Score 0.414 Round 5: 197 peptides, 34 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 176, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6884 reflections ( 99.41 % complete ) and 9190 restraints for refining 3971 atoms. 8518 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2026 (Rfree = 0.000) for 3971 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2110 (Rfree = 0.000) for 3951 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1576 (Rfree = 0.000) for 3934 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1530 (Rfree = 0.000) for 3916 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:54:13 GMT 2018 Job finished. TimeTaking 48.86 Used memory is bytes: 18292608