null Mon 24 Dec 00:22:20 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 2o62-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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/2o62-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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 00:22:24 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/2o62-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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 419 and 0 Target number of residues in the AU: 419 Target solvent content: 0.6113 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: 2o62-3.2-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: 2o62-3.2-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 3.200 Wilson plot Bfac: 57.41 10009 reflections ( 98.68 % complete ) and 0 restraints for refining 4827 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3713 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3626 (Rfree = 0.000) for 4827 atoms. Found 37 (43 requested) and removed 125 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 4758 seeds are put forward NCS extension: 0 residues added, 4758 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 10 peptides. Score 0.266 Round 2: 209 peptides, 40 chains. Longest chain 13 peptides. Score 0.325 Round 3: 242 peptides, 45 chains. Longest chain 9 peptides. Score 0.359 Round 4: 229 peptides, 40 chains. Longest chain 14 peptides. Score 0.383 Round 5: 243 peptides, 45 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 4 Chains 40, Residues 189, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 9095 restraints for refining 3944 atoms. 8357 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3528 (Rfree = 0.000) for 3944 atoms. Found 33 (35 requested) and removed 62 (17 requested) atoms. Cycle 2: After refmac, R = 0.3177 (Rfree = 0.000) for 3874 atoms. Found 32 (35 requested) and removed 26 (17 requested) atoms. Cycle 3: After refmac, R = 0.3282 (Rfree = 0.000) for 3859 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 4: After refmac, R = 0.3198 (Rfree = 0.000) for 3847 atoms. Found 34 (34 requested) and removed 35 (17 requested) atoms. Cycle 5: After refmac, R = 0.2683 (Rfree = 0.000) for 3834 atoms. Found 20 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.08 Search for helices and strands: 0 residues in 0 chains, 3900 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3925 seeds are put forward Round 1: 213 peptides, 46 chains. Longest chain 9 peptides. Score 0.260 Round 2: 238 peptides, 41 chains. Longest chain 11 peptides. Score 0.396 Round 3: 248 peptides, 41 chains. Longest chain 13 peptides. Score 0.423 Round 4: 232 peptides, 40 chains. Longest chain 17 peptides. Score 0.391 Round 5: 252 peptides, 41 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 5 Chains 41, Residues 211, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8577 restraints for refining 3874 atoms. 7705 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3106 (Rfree = 0.000) for 3874 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 7: After refmac, R = 0.3054 (Rfree = 0.000) for 3853 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 8: After refmac, R = 0.2995 (Rfree = 0.000) for 3852 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 9: After refmac, R = 0.3216 (Rfree = 0.000) for 3840 atoms. Found 34 (34 requested) and removed 39 (17 requested) atoms. Cycle 10: After refmac, R = 0.2932 (Rfree = 0.000) for 3822 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.07 Search for helices and strands: 0 residues in 0 chains, 3906 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3912 seeds are put forward Round 1: 228 peptides, 47 chains. Longest chain 10 peptides. Score 0.293 Round 2: 261 peptides, 46 chains. Longest chain 18 peptides. Score 0.400 Round 3: 259 peptides, 46 chains. Longest chain 12 peptides. Score 0.395 Round 4: 265 peptides, 44 chains. Longest chain 19 peptides. Score 0.434 Round 5: 257 peptides, 42 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Chains 43, Residues 215, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8799 restraints for refining 3944 atoms. 7920 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3009 (Rfree = 0.000) for 3944 atoms. Found 33 (35 requested) and removed 32 (17 requested) atoms. Cycle 12: After refmac, R = 0.2810 (Rfree = 0.000) for 3916 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 13: After refmac, R = 0.2453 (Rfree = 0.000) for 3903 atoms. Found 17 (35 requested) and removed 20 (17 requested) atoms. Cycle 14: After refmac, R = 0.2311 (Rfree = 0.000) for 3891 atoms. Found 13 (35 requested) and removed 21 (17 requested) atoms. Cycle 15: After refmac, R = 0.2628 (Rfree = 0.000) for 3879 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 3935 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3952 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 11 peptides. Score 0.315 Round 2: 247 peptides, 44 chains. Longest chain 10 peptides. Score 0.385 Round 3: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.422 Round 4: 257 peptides, 39 chains. Longest chain 15 peptides. Score 0.469 Round 5: 252 peptides, 39 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 4 Chains 41, Residues 218, Estimated correctness of the model 1.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8460 restraints for refining 3944 atoms. 7524 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2709 (Rfree = 0.000) for 3944 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 17: After refmac, R = 0.2685 (Rfree = 0.000) for 3923 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. Cycle 18: After refmac, R = 0.2286 (Rfree = 0.000) for 3915 atoms. Found 9 (35 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.2654 (Rfree = 0.000) for 3897 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 20: After refmac, R = 0.2518 (Rfree = 0.000) for 3898 atoms. Found 20 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 3935 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3950 seeds are put forward Round 1: 235 peptides, 46 chains. Longest chain 13 peptides. Score 0.327 Round 2: 253 peptides, 40 chains. Longest chain 13 peptides. Score 0.448 Round 3: 253 peptides, 40 chains. Longest chain 16 peptides. Score 0.448 Round 4: 249 peptides, 42 chains. Longest chain 13 peptides. Score 0.414 Round 5: 235 peptides, 39 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 3 Chains 40, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8665 restraints for refining 3944 atoms. 7853 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2950 (Rfree = 0.000) for 3944 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 22: After refmac, R = 0.2746 (Rfree = 0.000) for 3927 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 23: After refmac, R = 0.2911 (Rfree = 0.000) for 3922 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.2384 (Rfree = 0.000) for 3919 atoms. Found 16 (35 requested) and removed 22 (17 requested) atoms. Cycle 25: After refmac, R = 0.2139 (Rfree = 0.000) for 3901 atoms. Found 14 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.09 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3969 seeds are put forward Round 1: 238 peptides, 48 chains. Longest chain 14 peptides. Score 0.311 Round 2: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.367 Round 3: 266 peptides, 46 chains. Longest chain 10 peptides. Score 0.413 Round 4: 268 peptides, 45 chains. Longest chain 16 peptides. Score 0.430 Round 5: 282 peptides, 46 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 47, Residues 236, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8465 restraints for refining 3942 atoms. 7529 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2738 (Rfree = 0.000) for 3942 atoms. Found 32 (35 requested) and removed 22 (17 requested) atoms. Cycle 27: After refmac, R = 0.2606 (Rfree = 0.000) for 3939 atoms. Found 35 (35 requested) and removed 23 (17 requested) atoms. Cycle 28: After refmac, R = 0.2803 (Rfree = 0.000) for 3948 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 29: After refmac, R = 0.2599 (Rfree = 0.000) for 3947 atoms. Found 35 (35 requested) and removed 22 (17 requested) atoms. Cycle 30: After refmac, R = 0.2766 (Rfree = 0.000) for 3949 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 3.08 Search for helices and strands: 0 residues in 0 chains, 4044 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4059 seeds are put forward Round 1: 225 peptides, 45 chains. Longest chain 11 peptides. Score 0.309 Round 2: 258 peptides, 45 chains. Longest chain 12 peptides. Score 0.403 Round 3: 254 peptides, 44 chains. Longest chain 14 peptides. Score 0.404 Round 4: 243 peptides, 38 chains. Longest chain 15 peptides. Score 0.445 Round 5: 259 peptides, 43 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 39, Residues 205, Estimated correctness of the model 0.0 % 8 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8398 restraints for refining 3944 atoms. 7515 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2813 (Rfree = 0.000) for 3944 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 32: After refmac, R = 0.2956 (Rfree = 0.000) for 3938 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 33: After refmac, R = 0.2389 (Rfree = 0.000) for 3934 atoms. Found 17 (35 requested) and removed 21 (17 requested) atoms. Cycle 34: After refmac, R = 0.2519 (Rfree = 0.000) for 3924 atoms. Found 35 (35 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.2592 (Rfree = 0.000) for 3934 atoms. Found 35 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.09 Search for helices and strands: 0 residues in 0 chains, 3981 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3996 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 10 peptides. Score 0.290 Round 2: 224 peptides, 39 chains. Longest chain 13 peptides. Score 0.381 Round 3: 236 peptides, 40 chains. Longest chain 16 peptides. Score 0.402 Round 4: 246 peptides, 40 chains. Longest chain 15 peptides. Score 0.429 Round 5: 245 peptides, 39 chains. Longest chain 14 peptides. Score 0.438 Taking the results from Round 5 Chains 39, Residues 206, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8532 restraints for refining 3944 atoms. 7706 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2616 (Rfree = 0.000) for 3944 atoms. Found 24 (35 requested) and removed 20 (17 requested) atoms. Cycle 37: After refmac, R = 0.2498 (Rfree = 0.000) for 3934 atoms. Found 35 (35 requested) and removed 20 (17 requested) atoms. Cycle 38: After refmac, R = 0.2414 (Rfree = 0.000) for 3942 atoms. Found 21 (35 requested) and removed 21 (17 requested) atoms. Cycle 39: After refmac, R = 0.2470 (Rfree = 0.000) for 3937 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 40: After refmac, R = 0.2583 (Rfree = 0.000) for 3946 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 3.03 Search for helices and strands: 0 residues in 0 chains, 4014 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4030 seeds are put forward Round 1: 166 peptides, 35 chains. Longest chain 9 peptides. Score 0.256 Round 2: 197 peptides, 37 chains. Longest chain 12 peptides. Score 0.327 Round 3: 213 peptides, 37 chains. Longest chain 14 peptides. Score 0.374 Round 4: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.356 Round 5: 217 peptides, 36 chains. Longest chain 20 peptides. Score 0.398 Taking the results from Round 5 Chains 36, Residues 181, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8520 restraints for refining 3944 atoms. 7736 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2815 (Rfree = 0.000) for 3944 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 42: After refmac, R = 0.2595 (Rfree = 0.000) for 3943 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 43: After refmac, R = 0.2521 (Rfree = 0.000) for 3950 atoms. Found 31 (35 requested) and removed 21 (17 requested) atoms. Cycle 44: After refmac, R = 0.2430 (Rfree = 0.000) for 3958 atoms. Found 35 (35 requested) and removed 20 (17 requested) atoms. Cycle 45: After refmac, R = 0.2564 (Rfree = 0.000) for 3968 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.03 Search for helices and strands: 0 residues in 0 chains, 3988 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4009 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 8 peptides. Score 0.251 Round 2: 173 peptides, 31 chains. Longest chain 16 peptides. Score 0.333 Round 3: 172 peptides, 32 chains. Longest chain 13 peptides. Score 0.316 Round 4: 183 peptides, 35 chains. Longest chain 17 peptides. Score 0.311 Round 5: 190 peptides, 31 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 159, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2o62-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (159 residues) following loop building 5 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10009 reflections ( 98.68 % complete ) and 8487 restraints for refining 3944 atoms. 7782 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2631 (Rfree = 0.000) for 3944 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2819 (Rfree = 0.000) for 3916 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2394 (Rfree = 0.000) for 3885 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2085 (Rfree = 0.000) for 3863 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:07:39 GMT 2018 Job finished. TimeTaking 45.32 Used memory is bytes: 22548000