null Mon 24 Dec 07:27:24 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 1vkh-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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/1vkh-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 07:27:28 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/1vkh-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 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-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: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.4-parrot-noncs.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 4809 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3290 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2899 (Rfree = 0.000) for 4809 atoms. Found 36 (36 requested) and removed 93 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 3.35 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 0 residues added, 4890 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 10 peptides. Score 0.273 Round 2: 256 peptides, 45 chains. Longest chain 12 peptides. Score 0.425 Round 3: 266 peptides, 43 chains. Longest chain 12 peptides. Score 0.479 Round 4: 284 peptides, 44 chains. Longest chain 13 peptides. Score 0.517 Round 5: 295 peptides, 44 chains. Longest chain 13 peptides. Score 0.546 Taking the results from Round 5 Chains 44, Residues 251, Estimated correctness of the model 10.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8925 restraints for refining 3970 atoms. 7965 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2358 (Rfree = 0.000) for 3970 atoms. Found 16 (29 requested) and removed 36 (14 requested) atoms. Cycle 2: After refmac, R = 0.2201 (Rfree = 0.000) for 3906 atoms. Found 18 (29 requested) and removed 29 (14 requested) atoms. Cycle 3: After refmac, R = 0.2070 (Rfree = 0.000) for 3886 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2019 (Rfree = 0.000) for 3873 atoms. Found 8 (29 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.1957 (Rfree = 0.000) for 3853 atoms. Found 20 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 4028 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4042 seeds are put forward Round 1: 250 peptides, 47 chains. Longest chain 13 peptides. Score 0.380 Round 2: 272 peptides, 43 chains. Longest chain 16 peptides. Score 0.496 Round 3: 291 peptides, 47 chains. Longest chain 16 peptides. Score 0.501 Round 4: 299 peptides, 43 chains. Longest chain 21 peptides. Score 0.567 Round 5: 301 peptides, 41 chains. Longest chain 22 peptides. Score 0.593 Taking the results from Round 5 Chains 41, Residues 260, Estimated correctness of the model 26.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8803 restraints for refining 3971 atoms. 7717 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2100 (Rfree = 0.000) for 3971 atoms. Found 23 (29 requested) and removed 32 (14 requested) atoms. Cycle 7: After refmac, R = 0.1896 (Rfree = 0.000) for 3955 atoms. Found 15 (29 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.1849 (Rfree = 0.000) for 3948 atoms. Found 10 (29 requested) and removed 22 (14 requested) atoms. Cycle 9: After refmac, R = 0.1924 (Rfree = 0.000) for 3936 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.1858 (Rfree = 0.000) for 3928 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 4085 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4105 seeds are put forward Round 1: 258 peptides, 46 chains. Longest chain 12 peptides. Score 0.418 Round 2: 282 peptides, 43 chains. Longest chain 16 peptides. Score 0.523 Round 3: 298 peptides, 42 chains. Longest chain 18 peptides. Score 0.575 Round 4: 299 peptides, 40 chains. Longest chain 18 peptides. Score 0.599 Round 5: 301 peptides, 40 chains. Longest chain 20 peptides. Score 0.603 Taking the results from Round 5 Chains 40, Residues 261, Estimated correctness of the model 29.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8950 restraints for refining 3971 atoms. 7946 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 3971 atoms. Found 25 (29 requested) and removed 20 (14 requested) atoms. Cycle 12: After refmac, R = 0.2080 (Rfree = 0.000) for 3971 atoms. Found 18 (30 requested) and removed 20 (15 requested) atoms. Cycle 13: After refmac, R = 0.2021 (Rfree = 0.000) for 3965 atoms. Found 13 (29 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.1981 (Rfree = 0.000) for 3956 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.1907 (Rfree = 0.000) for 3948 atoms. Found 10 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 4091 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4104 seeds are put forward Round 1: 247 peptides, 44 chains. Longest chain 20 peptides. Score 0.410 Round 2: 282 peptides, 44 chains. Longest chain 15 peptides. Score 0.512 Round 3: 301 peptides, 45 chains. Longest chain 16 peptides. Score 0.550 Round 4: 302 peptides, 44 chains. Longest chain 23 peptides. Score 0.564 Round 5: 309 peptides, 45 chains. Longest chain 18 peptides. Score 0.570 Taking the results from Round 5 Chains 45, Residues 264, Estimated correctness of the model 18.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8968 restraints for refining 3971 atoms. 7936 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2186 (Rfree = 0.000) for 3971 atoms. Found 15 (29 requested) and removed 23 (14 requested) atoms. Cycle 17: After refmac, R = 0.1961 (Rfree = 0.000) for 3957 atoms. Found 5 (29 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 3938 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 3929 atoms. Found 18 (29 requested) and removed 19 (14 requested) atoms. Cycle 20: After refmac, R = 0.1905 (Rfree = 0.000) for 3925 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 4082 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4106 seeds are put forward Round 1: 247 peptides, 45 chains. Longest chain 12 peptides. Score 0.397 Round 2: 267 peptides, 42 chains. Longest chain 14 peptides. Score 0.494 Round 3: 277 peptides, 41 chains. Longest chain 17 peptides. Score 0.533 Round 4: 275 peptides, 44 chains. Longest chain 16 peptides. Score 0.493 Round 5: 274 peptides, 40 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 5 Chains 40, Residues 234, Estimated correctness of the model 6.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9274 restraints for refining 3970 atoms. 8378 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2318 (Rfree = 0.000) for 3970 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 22: After refmac, R = 0.2144 (Rfree = 0.000) for 3968 atoms. Found 18 (30 requested) and removed 17 (15 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 3963 atoms. Found 12 (29 requested) and removed 19 (14 requested) atoms. Cycle 24: After refmac, R = 0.1837 (Rfree = 0.000) for 3954 atoms. Found 5 (29 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.1764 (Rfree = 0.000) for 3943 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 4086 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4103 seeds are put forward Round 1: 231 peptides, 45 chains. Longest chain 10 peptides. Score 0.346 Round 2: 280 peptides, 43 chains. Longest chain 13 peptides. Score 0.518 Round 3: 268 peptides, 49 chains. Longest chain 15 peptides. Score 0.410 Round 4: 265 peptides, 41 chains. Longest chain 14 peptides. Score 0.501 Round 5: 264 peptides, 44 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 2 Chains 43, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9118 restraints for refining 3971 atoms. 8213 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2151 (Rfree = 0.000) for 3971 atoms. Found 15 (29 requested) and removed 19 (14 requested) atoms. Cycle 27: After refmac, R = 0.2099 (Rfree = 0.000) for 3961 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2009 (Rfree = 0.000) for 3957 atoms. Found 20 (29 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.1967 (Rfree = 0.000) for 3958 atoms. Found 15 (29 requested) and removed 17 (14 requested) atoms. Cycle 30: After refmac, R = 0.2013 (Rfree = 0.000) for 3951 atoms. Found 17 (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, 4087 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4105 seeds are put forward Round 1: 230 peptides, 46 chains. Longest chain 10 peptides. Score 0.329 Round 2: 266 peptides, 47 chains. Longest chain 11 peptides. Score 0.429 Round 3: 275 peptides, 42 chains. Longest chain 17 peptides. Score 0.516 Round 4: 272 peptides, 43 chains. Longest chain 17 peptides. Score 0.496 Round 5: 261 peptides, 41 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 3 Chains 44, Residues 233, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9053 restraints for refining 3970 atoms. 8102 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2236 (Rfree = 0.000) for 3970 atoms. Found 25 (29 requested) and removed 26 (14 requested) atoms. Cycle 32: After refmac, R = 0.2145 (Rfree = 0.000) for 3954 atoms. Found 20 (29 requested) and removed 19 (14 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 3953 atoms. Found 24 (29 requested) and removed 18 (14 requested) atoms. Cycle 34: After refmac, R = 0.2070 (Rfree = 0.000) for 3958 atoms. Found 18 (29 requested) and removed 16 (14 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 3957 atoms. Found 23 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 4112 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 4123 seeds are put forward Round 1: 205 peptides, 41 chains. Longest chain 10 peptides. Score 0.315 Round 2: 223 peptides, 38 chains. Longest chain 11 peptides. Score 0.416 Round 3: 242 peptides, 37 chains. Longest chain 15 peptides. Score 0.485 Round 4: 237 peptides, 39 chains. Longest chain 13 peptides. Score 0.445 Round 5: 240 peptides, 36 chains. Longest chain 14 peptides. Score 0.492 Taking the results from Round 5 Chains 36, Residues 204, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9311 restraints for refining 3971 atoms. 8486 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 3971 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.2081 (Rfree = 0.000) for 3974 atoms. Found 25 (30 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.2070 (Rfree = 0.000) for 3977 atoms. Found 27 (30 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.1994 (Rfree = 0.000) for 3984 atoms. Found 29 (30 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.1960 (Rfree = 0.000) for 3996 atoms. Found 24 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 4114 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4129 seeds are put forward Round 1: 173 peptides, 34 chains. Longest chain 14 peptides. Score 0.307 Round 2: 220 peptides, 38 chains. Longest chain 11 peptides. Score 0.406 Round 3: 206 peptides, 37 chains. Longest chain 13 peptides. Score 0.375 Round 4: 214 peptides, 34 chains. Longest chain 11 peptides. Score 0.441 Round 5: 198 peptides, 35 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 4 Chains 34, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9373 restraints for refining 3971 atoms. 8687 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2185 (Rfree = 0.000) for 3971 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 42: After refmac, R = 0.1891 (Rfree = 0.000) for 3964 atoms. Found 20 (30 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.1621 (Rfree = 0.000) for 3967 atoms. Found 6 (29 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.1562 (Rfree = 0.000) for 3954 atoms. Found 3 (29 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1542 (Rfree = 0.000) for 3942 atoms. Found 4 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 4053 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 4056 seeds are put forward Round 1: 157 peptides, 30 chains. Longest chain 10 peptides. Score 0.310 Round 2: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.367 Round 3: 190 peptides, 31 chains. Longest chain 11 peptides. Score 0.407 Round 4: 193 peptides, 30 chains. Longest chain 13 peptides. Score 0.431 Round 5: 194 peptides, 33 chains. Longest chain 10 peptides. Score 0.392 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 163, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 7 % 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 9323 restraints for refining 3971 atoms. 8652 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1940 (Rfree = 0.000) for 3971 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1993 (Rfree = 0.000) for 3950 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2061 (Rfree = 0.000) for 3933 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1646 (Rfree = 0.000) for 3917 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:12:20 GMT 2018 Job finished. TimeTaking 44.94 Used memory is bytes: 14738192