null Mon 24 Dec 00:31:04 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 2o62-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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/2o62-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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 00:31:09 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/2o62-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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 401 and 0 Target number of residues in the AU: 401 Target solvent content: 0.6280 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-3.6-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 target number of atoms Had to go as low as 0.70 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: 66.305 3.600 Wilson plot Bfac: 65.28 7057 reflections ( 98.22 % complete ) and 0 restraints for refining 4789 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3714 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 4789 atoms. Found 30 (30 requested) and removed 146 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 4703 seeds are put forward NCS extension: 0 residues added, 4703 seeds are put forward Round 1: 190 peptides, 41 chains. Longest chain 8 peptides. Score 0.253 Round 2: 229 peptides, 45 chains. Longest chain 10 peptides. Score 0.321 Round 3: 230 peptides, 41 chains. Longest chain 14 peptides. Score 0.373 Round 4: 237 peptides, 44 chains. Longest chain 10 peptides. Score 0.357 Round 5: 225 peptides, 41 chains. Longest chain 14 peptides. Score 0.359 Taking the results from Round 3 Chains 41, Residues 189, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 8884 restraints for refining 3915 atoms. 8057 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2938 (Rfree = 0.000) for 3915 atoms. Found 13 (25 requested) and removed 32 (12 requested) atoms. Cycle 2: After refmac, R = 0.3085 (Rfree = 0.000) for 3841 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 3: After refmac, R = 0.2711 (Rfree = 0.000) for 3812 atoms. Found 4 (24 requested) and removed 23 (12 requested) atoms. Cycle 4: After refmac, R = 0.2717 (Rfree = 0.000) for 3761 atoms. Found 11 (24 requested) and removed 17 (12 requested) atoms. Cycle 5: After refmac, R = 0.2663 (Rfree = 0.000) for 3741 atoms. Found 6 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 3785 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3808 seeds are put forward Round 1: 193 peptides, 42 chains. Longest chain 8 peptides. Score 0.249 Round 2: 236 peptides, 46 chains. Longest chain 9 peptides. Score 0.330 Round 3: 236 peptides, 44 chains. Longest chain 11 peptides. Score 0.354 Round 4: 238 peptides, 41 chains. Longest chain 10 peptides. Score 0.396 Round 5: 245 peptides, 43 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 4 Chains 41, Residues 197, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9055 restraints for refining 3915 atoms. 8264 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3085 (Rfree = 0.000) for 3915 atoms. Found 24 (25 requested) and removed 39 (12 requested) atoms. Cycle 7: After refmac, R = 0.2856 (Rfree = 0.000) for 3872 atoms. Found 24 (25 requested) and removed 22 (12 requested) atoms. Cycle 8: After refmac, R = 0.3053 (Rfree = 0.000) for 3850 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 9: After refmac, R = 0.2970 (Rfree = 0.000) for 3820 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 10: After refmac, R = 0.2981 (Rfree = 0.000) for 3784 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3857 seeds are put forward NCS extension: 0 residues added, 3857 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 12 peptides. Score 0.298 Round 2: 245 peptides, 41 chains. Longest chain 12 peptides. Score 0.415 Round 3: 249 peptides, 40 chains. Longest chain 10 peptides. Score 0.437 Round 4: 238 peptides, 36 chains. Longest chain 19 peptides. Score 0.455 Round 5: 247 peptides, 34 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 5 Chains 35, Residues 213, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 8973 restraints for refining 3915 atoms. 8107 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3001 (Rfree = 0.000) for 3915 atoms. Found 22 (25 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.2944 (Rfree = 0.000) for 3874 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 13: After refmac, R = 0.2830 (Rfree = 0.000) for 3859 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 14: After refmac, R = 0.2757 (Rfree = 0.000) for 3846 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 15: After refmac, R = 0.2682 (Rfree = 0.000) for 3831 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3902 seeds are put forward Round 1: 203 peptides, 44 chains. Longest chain 8 peptides. Score 0.255 Round 2: 240 peptides, 42 chains. Longest chain 17 peptides. Score 0.389 Round 3: 239 peptides, 43 chains. Longest chain 14 peptides. Score 0.375 Round 4: 245 peptides, 41 chains. Longest chain 14 peptides. Score 0.415 Round 5: 235 peptides, 39 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 4 Chains 41, Residues 204, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9108 restraints for refining 3916 atoms. 8301 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2781 (Rfree = 0.000) for 3916 atoms. Found 19 (25 requested) and removed 36 (12 requested) atoms. Cycle 17: After refmac, R = 0.2672 (Rfree = 0.000) for 3878 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 18: After refmac, R = 0.2268 (Rfree = 0.000) for 3857 atoms. Found 9 (24 requested) and removed 17 (12 requested) atoms. Cycle 19: After refmac, R = 0.2597 (Rfree = 0.000) for 3839 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 20: After refmac, R = 0.2282 (Rfree = 0.000) for 3825 atoms. Found 4 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3866 seeds are put forward Round 1: 217 peptides, 46 chains. Longest chain 10 peptides. Score 0.273 Round 2: 227 peptides, 40 chains. Longest chain 13 peptides. Score 0.377 Round 3: 240 peptides, 44 chains. Longest chain 16 peptides. Score 0.365 Round 4: 229 peptides, 42 chains. Longest chain 10 peptides. Score 0.358 Round 5: 235 peptides, 42 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 2 Chains 40, Residues 187, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9008 restraints for refining 3887 atoms. 8265 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2542 (Rfree = 0.000) for 3887 atoms. Found 17 (24 requested) and removed 25 (12 requested) atoms. Cycle 22: After refmac, R = 0.2710 (Rfree = 0.000) for 3866 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 23: After refmac, R = 0.2662 (Rfree = 0.000) for 3848 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 24: After refmac, R = 0.2652 (Rfree = 0.000) for 3833 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 25: After refmac, R = 0.2611 (Rfree = 0.000) for 3828 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3880 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3896 seeds are put forward Round 1: 193 peptides, 40 chains. Longest chain 7 peptides. Score 0.276 Round 2: 217 peptides, 40 chains. Longest chain 12 peptides. Score 0.348 Round 3: 215 peptides, 42 chains. Longest chain 9 peptides. Score 0.317 Round 4: 236 peptides, 44 chains. Longest chain 11 peptides. Score 0.354 Round 5: 229 peptides, 41 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 5 Chains 41, Residues 188, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 8979 restraints for refining 3916 atoms. 8213 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2740 (Rfree = 0.000) for 3916 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 27: After refmac, R = 0.2650 (Rfree = 0.000) for 3890 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 28: After refmac, R = 0.2171 (Rfree = 0.000) for 3865 atoms. Found 9 (24 requested) and removed 23 (12 requested) atoms. Cycle 29: After refmac, R = 0.2053 (Rfree = 0.000) for 3845 atoms. Found 6 (24 requested) and removed 17 (12 requested) atoms. Cycle 30: After refmac, R = 0.2040 (Rfree = 0.000) for 3829 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3866 seeds are put forward Round 1: 186 peptides, 41 chains. Longest chain 9 peptides. Score 0.240 Round 2: 234 peptides, 46 chains. Longest chain 11 peptides. Score 0.324 Round 3: 239 peptides, 44 chains. Longest chain 11 peptides. Score 0.363 Round 4: 222 peptides, 40 chains. Longest chain 10 peptides. Score 0.363 Round 5: 226 peptides, 43 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 4 Chains 40, Residues 182, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9027 restraints for refining 3916 atoms. 8309 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2438 (Rfree = 0.000) for 3916 atoms. Found 16 (25 requested) and removed 16 (12 requested) atoms. Cycle 32: After refmac, R = 0.2510 (Rfree = 0.000) for 3891 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 33: After refmac, R = 0.2529 (Rfree = 0.000) for 3887 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 34: After refmac, R = 0.2040 (Rfree = 0.000) for 3871 atoms. Found 18 (24 requested) and removed 15 (12 requested) atoms. Cycle 35: After refmac, R = 0.1987 (Rfree = 0.000) for 3865 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 3890 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3902 seeds are put forward Round 1: 181 peptides, 40 chains. Longest chain 9 peptides. Score 0.237 Round 2: 200 peptides, 39 chains. Longest chain 7 peptides. Score 0.310 Round 3: 205 peptides, 38 chains. Longest chain 12 peptides. Score 0.338 Round 4: 211 peptides, 36 chains. Longest chain 13 peptides. Score 0.381 Round 5: 193 peptides, 37 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Chains 36, Residues 175, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9025 restraints for refining 3916 atoms. 8335 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2498 (Rfree = 0.000) for 3916 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 37: After refmac, R = 0.2549 (Rfree = 0.000) for 3895 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 38: After refmac, R = 0.2272 (Rfree = 0.000) for 3870 atoms. Found 18 (24 requested) and removed 18 (12 requested) atoms. Cycle 39: After refmac, R = 0.2310 (Rfree = 0.000) for 3864 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 40: After refmac, R = 0.2576 (Rfree = 0.000) for 3857 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 3895 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3917 seeds are put forward Round 1: 136 peptides, 32 chains. Longest chain 5 peptides. Score 0.196 Round 2: 184 peptides, 36 chains. Longest chain 10 peptides. Score 0.300 Round 3: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.308 Round 4: 183 peptides, 31 chains. Longest chain 12 peptides. Score 0.363 Round 5: 178 peptides, 32 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 4 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9002 restraints for refining 3901 atoms. 8396 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2594 (Rfree = 0.000) for 3901 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 42: After refmac, R = 0.2535 (Rfree = 0.000) for 3881 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 43: After refmac, R = 0.2445 (Rfree = 0.000) for 3873 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.2023 (Rfree = 0.000) for 3878 atoms. Found 15 (24 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1990 (Rfree = 0.000) for 3872 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 3898 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3909 seeds are put forward Round 1: 157 peptides, 34 chains. Longest chain 7 peptides. Score 0.240 Round 2: 177 peptides, 33 chains. Longest chain 10 peptides. Score 0.319 Round 3: 181 peptides, 31 chains. Longest chain 12 peptides. Score 0.357 Round 4: 181 peptides, 34 chains. Longest chain 10 peptides. Score 0.318 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 171, 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 2o62-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7057 reflections ( 98.22 % complete ) and 9090 restraints for refining 3916 atoms. 8440 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2602 (Rfree = 0.000) for 3916 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2568 (Rfree = 0.000) for 3888 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2038 (Rfree = 0.000) for 3866 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1904 (Rfree = 0.000) for 3849 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:15:24 GMT 2018 Job finished. TimeTaking 44.33 Used memory is bytes: 14630168