Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4p-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-parrot-hancs/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 373 and 0 Target number of residues in the AU: 373 Target solvent content: 0.6398 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.8-parrot-hancs.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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 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: 21.543 3.800 Wilson plot Bfac: 71.67 5384 reflections ( 99.39 % complete ) and 0 restraints for refining 5187 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3356 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3444 (Rfree = 0.000) for 5187 atoms. Found 28 (28 requested) and removed 78 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 5207 seeds are put forward NCS extension: 0 residues added, 5207 seeds are put forward Round 1: 154 peptides, 33 chains. Longest chain 8 peptides. Score 0.247 Round 2: 220 peptides, 40 chains. Longest chain 10 peptides. Score 0.363 Round 3: 241 peptides, 43 chains. Longest chain 10 peptides. Score 0.387 Round 4: 267 peptides, 43 chains. Longest chain 17 peptides. Score 0.459 Round 5: 281 peptides, 46 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 5 Chains 46, Residues 235, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 10110 restraints for refining 4254 atoms. 9145 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3104 (Rfree = 0.000) for 4254 atoms. Found 23 (23 requested) and removed 90 (11 requested) atoms. Cycle 2: After refmac, R = 0.3123 (Rfree = 0.000) for 4117 atoms. Found 23 (23 requested) and removed 83 (11 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2960 (Rfree = 0.000) for 3985 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 4: After refmac, R = 0.3225 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 58 (10 requested) atoms. Cycle 5: After refmac, R = 0.2884 (Rfree = 0.000) for 3835 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 3954 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3975 seeds are put forward Round 1: 196 peptides, 41 chains. Longest chain 9 peptides. Score 0.275 Round 2: 255 peptides, 47 chains. Longest chain 14 peptides. Score 0.378 Round 3: 273 peptides, 47 chains. Longest chain 13 peptides. Score 0.429 Round 4: 273 peptides, 43 chains. Longest chain 15 peptides. Score 0.475 Round 5: 304 peptides, 45 chains. Longest chain 17 peptides. Score 0.530 Taking the results from Round 5 Chains 45, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8886 restraints for refining 3900 atoms. 7895 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2896 (Rfree = 0.000) for 3900 atoms. Found 21 (21 requested) and removed 68 (10 requested) atoms. Cycle 7: After refmac, R = 0.2972 (Rfree = 0.000) for 3820 atoms. Found 21 (21 requested) and removed 89 (10 requested) atoms. Cycle 8: After refmac, R = 0.2848 (Rfree = 0.000) for 3713 atoms. Found 20 (20 requested) and removed 49 (10 requested) atoms. Cycle 9: After refmac, R = 0.2751 (Rfree = 0.000) for 3657 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 10: After refmac, R = 0.2700 (Rfree = 0.000) for 3613 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3717 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3737 seeds are put forward Round 1: 223 peptides, 44 chains. Longest chain 12 peptides. Score 0.321 Round 2: 249 peptides, 45 chains. Longest chain 16 peptides. Score 0.385 Round 3: 252 peptides, 44 chains. Longest chain 12 peptides. Score 0.406 Round 4: 283 peptides, 47 chains. Longest chain 13 peptides. Score 0.455 Round 5: 274 peptides, 40 chains. Longest chain 14 peptides. Score 0.510 Taking the results from Round 5 Chains 41, Residues 234, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8812 restraints for refining 3937 atoms. 7852 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3003 (Rfree = 0.000) for 3937 atoms. Found 21 (21 requested) and removed 147 (10 requested) atoms. Cycle 12: After refmac, R = 0.2935 (Rfree = 0.000) for 3762 atoms. Found 20 (20 requested) and removed 92 (10 requested) atoms. Cycle 13: After refmac, R = 0.2773 (Rfree = 0.000) for 3641 atoms. Found 20 (20 requested) and removed 46 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2114 (Rfree = 0.000) for 3591 atoms. Found 14 (19 requested) and removed 29 (9 requested) atoms. Cycle 15: After refmac, R = 0.2528 (Rfree = 0.000) for 3566 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 3671 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3686 seeds are put forward Round 1: 219 peptides, 42 chains. Longest chain 11 peptides. Score 0.334 Round 2: 247 peptides, 45 chains. Longest chain 11 peptides. Score 0.380 Round 3: 241 peptides, 41 chains. Longest chain 12 peptides. Score 0.411 Round 4: 241 peptides, 43 chains. Longest chain 13 peptides. Score 0.387 Round 5: 250 peptides, 43 chains. Longest chain 10 peptides. Score 0.413 Taking the results from Round 5 Chains 43, Residues 207, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 9046 restraints for refining 3940 atoms. 8229 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2851 (Rfree = 0.000) for 3940 atoms. Found 21 (21 requested) and removed 104 (10 requested) atoms. Cycle 17: After refmac, R = 0.2830 (Rfree = 0.000) for 3824 atoms. Found 21 (21 requested) and removed 76 (10 requested) atoms. Cycle 18: After refmac, R = 0.2484 (Rfree = 0.000) for 3746 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 19: After refmac, R = 0.2367 (Rfree = 0.000) for 3709 atoms. Found 20 (20 requested) and removed 39 (10 requested) atoms. Cycle 20: After refmac, R = 0.2372 (Rfree = 0.000) for 3673 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 3790 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3802 seeds are put forward Round 1: 200 peptides, 45 chains. Longest chain 7 peptides. Score 0.234 Round 2: 229 peptides, 42 chains. Longest chain 11 peptides. Score 0.364 Round 3: 247 peptides, 44 chains. Longest chain 12 peptides. Score 0.392 Round 4: 235 peptides, 43 chains. Longest chain 10 peptides. Score 0.369 Round 5: 224 peptides, 40 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 3 Chains 44, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8448 restraints for refining 3778 atoms. 7680 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2551 (Rfree = 0.000) for 3778 atoms. Found 20 (20 requested) and removed 57 (10 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 3710 atoms. Found 20 (20 requested) and removed 39 (10 requested) atoms. Cycle 23: After refmac, R = 0.2329 (Rfree = 0.000) for 3671 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 24: After refmac, R = 0.2384 (Rfree = 0.000) for 3646 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 25: After refmac, R = 0.2308 (Rfree = 0.000) for 3616 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 3738 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3756 seeds are put forward Round 1: 155 peptides, 35 chains. Longest chain 7 peptides. Score 0.221 Round 2: 178 peptides, 30 chains. Longest chain 21 peptides. Score 0.367 Round 3: 200 peptides, 38 chains. Longest chain 8 peptides. Score 0.328 Round 4: 212 peptides, 38 chains. Longest chain 14 peptides. Score 0.365 Round 5: 206 peptides, 37 chains. Longest chain 15 peptides. Score 0.360 Taking the results from Round 2 Chains 30, Residues 148, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 7901 restraints for refining 3535 atoms. 7306 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2520 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 27: After refmac, R = 0.2488 (Rfree = 0.000) for 3493 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 28: After refmac, R = 0.2483 (Rfree = 0.000) for 3455 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 29: After refmac, R = 0.2359 (Rfree = 0.000) for 3434 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 30: After refmac, R = 0.2653 (Rfree = 0.000) for 3416 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 3506 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 3539 seeds are put forward Round 1: 147 peptides, 35 chains. Longest chain 7 peptides. Score 0.193 Round 2: 197 peptides, 37 chains. Longest chain 15 peptides. Score 0.332 Round 3: 210 peptides, 35 chains. Longest chain 12 peptides. Score 0.397 Round 4: 199 peptides, 38 chains. Longest chain 10 peptides. Score 0.325 Round 5: 216 peptides, 38 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 3 Chains 35, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 6993 restraints for refining 3325 atoms. 6328 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2622 (Rfree = 0.000) for 3325 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 32: After refmac, R = 0.2581 (Rfree = 0.000) for 3294 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 33: After refmac, R = 0.2432 (Rfree = 0.000) for 3263 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 34: After refmac, R = 0.2642 (Rfree = 0.000) for 3238 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 35: After refmac, R = 0.2555 (Rfree = 0.000) for 3216 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 3347 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3360 seeds are put forward Round 1: 157 peptides, 36 chains. Longest chain 6 peptides. Score 0.214 Round 2: 222 peptides, 44 chains. Longest chain 15 peptides. Score 0.318 Round 3: 202 peptides, 37 chains. Longest chain 9 peptides. Score 0.347 Round 4: 210 peptides, 39 chains. Longest chain 8 peptides. Score 0.346 Round 5: 208 peptides, 39 chains. Longest chain 9 peptides. Score 0.340 Taking the results from Round 3 Chains 37, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 6898 restraints for refining 3236 atoms. 6275 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3029 (Rfree = 0.000) for 3236 atoms. Found 17 (17 requested) and removed 52 (8 requested) atoms. Cycle 37: After refmac, R = 0.2887 (Rfree = 0.000) for 3168 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 38: After refmac, R = 0.2800 (Rfree = 0.000) for 3138 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.2722 (Rfree = 0.000) for 3120 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 40: After refmac, R = 0.2497 (Rfree = 0.000) for 3102 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3174 seeds are put forward NCS extension: 0 residues added, 3174 seeds are put forward Round 1: 166 peptides, 37 chains. Longest chain 7 peptides. Score 0.231 Round 2: 198 peptides, 41 chains. Longest chain 8 peptides. Score 0.282 Round 3: 218 peptides, 40 chains. Longest chain 12 peptides. Score 0.357 Round 4: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.347 Round 5: 214 peptides, 37 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 37, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 6988 restraints for refining 3301 atoms. 6317 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2801 (Rfree = 0.000) for 3301 atoms. Found 18 (18 requested) and removed 59 (9 requested) atoms. Cycle 42: After refmac, R = 0.2729 (Rfree = 0.000) for 3237 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 43: After refmac, R = 0.2500 (Rfree = 0.000) for 3202 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2462 (Rfree = 0.000) for 3187 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 45: After refmac, R = 0.2488 (Rfree = 0.000) for 3173 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3296 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3311 seeds are put forward Round 1: 149 peptides, 34 chains. Longest chain 8 peptides. Score 0.214 Round 2: 187 peptides, 36 chains. Longest chain 10 peptides. Score 0.314 Round 3: 190 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Round 4: 194 peptides, 34 chains. Longest chain 12 peptides. Score 0.362 Round 5: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 168, 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 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5384 reflections ( 99.39 % complete ) and 6845 restraints for refining 3244 atoms. 6207 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2791 (Rfree = 0.000) for 3244 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2799 (Rfree = 0.000) for 3215 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2633 (Rfree = 0.000) for 3188 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2644 (Rfree = 0.000) for 3169 atoms. TimeTaking 61.17