Mon 24 Dec 00:09:10 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 2ffj-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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/2ffj-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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 00:09:14 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/2ffj-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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 407 and 0 Target number of residues in the AU: 407 Target solvent content: 0.6717 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-4.0-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: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4800 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: 29.898 4.000 Wilson plot Bfac: 93.41 5972 reflections ( 98.65 % complete ) and 0 restraints for refining 5312 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3454 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3967 (Rfree = 0.000) for 5312 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 5443 seeds are put forward NCS extension: 0 residues added, 5443 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 9 peptides. Score 0.251 Round 2: 251 peptides, 43 chains. Longest chain 15 peptides. Score 0.384 Round 3: 277 peptides, 45 chains. Longest chain 17 peptides. Score 0.426 Round 4: 282 peptides, 34 chains. Longest chain 22 peptides. Score 0.544 Round 5: 288 peptides, 40 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 4 Chains 35, Residues 248, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9378 restraints for refining 4118 atoms. 8350 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3080 (Rfree = 0.000) for 4118 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 2: After refmac, R = 0.2792 (Rfree = 0.000) for 3979 atoms. Found 14 (19 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.2705 (Rfree = 0.000) for 3914 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 4: After refmac, R = 0.2744 (Rfree = 0.000) for 3846 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 5: After refmac, R = 0.2785 (Rfree = 0.000) for 3803 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 3976 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 4003 seeds are put forward Round 1: 243 peptides, 46 chains. Longest chain 8 peptides. Score 0.332 Round 2: 260 peptides, 41 chains. Longest chain 16 peptides. Score 0.427 Round 3: 278 peptides, 40 chains. Longest chain 17 peptides. Score 0.478 Round 4: 292 peptides, 40 chains. Longest chain 15 peptides. Score 0.508 Round 5: 304 peptides, 39 chains. Longest chain 18 peptides. Score 0.542 Taking the results from Round 5 Chains 39, Residues 265, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8786 restraints for refining 3958 atoms. 7696 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3010 (Rfree = 0.000) for 3958 atoms. Found 18 (18 requested) and removed 49 (9 requested) atoms. Cycle 7: After refmac, R = 0.2777 (Rfree = 0.000) for 3870 atoms. Found 15 (18 requested) and removed 41 (9 requested) atoms. Cycle 8: After refmac, R = 0.2646 (Rfree = 0.000) for 3808 atoms. Found 13 (18 requested) and removed 29 (9 requested) atoms. Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 3750 atoms. Found 6 (18 requested) and removed 20 (9 requested) atoms. Cycle 10: After refmac, R = 0.2117 (Rfree = 0.000) for 3720 atoms. Found 2 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3927 seeds are put forward Round 1: 236 peptides, 46 chains. Longest chain 11 peptides. Score 0.313 Round 2: 281 peptides, 44 chains. Longest chain 12 peptides. Score 0.445 Round 3: 287 peptides, 42 chains. Longest chain 16 peptides. Score 0.478 Round 4: 281 peptides, 35 chains. Longest chain 21 peptides. Score 0.533 Round 5: 279 peptides, 38 chains. Longest chain 20 peptides. Score 0.500 Taking the results from Round 4 Chains 35, Residues 246, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9032 restraints for refining 4003 atoms. 8025 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2486 (Rfree = 0.000) for 4003 atoms. Found 12 (19 requested) and removed 41 (9 requested) atoms. Cycle 12: After refmac, R = 0.2399 (Rfree = 0.000) for 3922 atoms. Found 10 (18 requested) and removed 31 (9 requested) atoms. Cycle 13: After refmac, R = 0.2393 (Rfree = 0.000) for 3881 atoms. Found 17 (18 requested) and removed 28 (9 requested) atoms. Cycle 14: After refmac, R = 0.2436 (Rfree = 0.000) for 3846 atoms. Found 14 (18 requested) and removed 25 (9 requested) atoms. Cycle 15: After refmac, R = 0.2359 (Rfree = 0.000) for 3812 atoms. Found 10 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 3980 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 4011 seeds are put forward Round 1: 232 peptides, 44 chains. Longest chain 12 peptides. Score 0.325 Round 2: 260 peptides, 39 chains. Longest chain 30 peptides. Score 0.448 Round 3: 261 peptides, 42 chains. Longest chain 17 peptides. Score 0.419 Round 4: 266 peptides, 39 chains. Longest chain 15 peptides. Score 0.461 Round 5: 265 peptides, 41 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 4 Chains 39, Residues 227, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8938 restraints for refining 3963 atoms. 8038 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2942 (Rfree = 0.000) for 3963 atoms. Found 18 (18 requested) and removed 57 (9 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2577 (Rfree = 0.000) for 3884 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 18: After refmac, R = 0.2579 (Rfree = 0.000) for 3838 atoms. Found 13 (18 requested) and removed 22 (9 requested) atoms. Cycle 19: After refmac, R = 0.2573 (Rfree = 0.000) for 3811 atoms. Found 13 (18 requested) and removed 26 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2564 (Rfree = 0.000) for 3776 atoms. Found 13 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3983 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4003 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 15 peptides. Score 0.290 Round 2: 263 peptides, 44 chains. Longest chain 17 peptides. Score 0.403 Round 3: 267 peptides, 41 chains. Longest chain 18 peptides. Score 0.443 Round 4: 273 peptides, 40 chains. Longest chain 16 peptides. Score 0.467 Round 5: 260 peptides, 39 chains. Longest chain 13 peptides. Score 0.448 Taking the results from Round 4 Chains 40, Residues 233, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8529 restraints for refining 3918 atoms. 7589 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2745 (Rfree = 0.000) for 3918 atoms. Found 15 (18 requested) and removed 40 (9 requested) atoms. Cycle 22: After refmac, R = 0.2418 (Rfree = 0.000) for 3868 atoms. Found 10 (18 requested) and removed 21 (9 requested) atoms. Cycle 23: After refmac, R = 0.2189 (Rfree = 0.000) for 3839 atoms. Found 6 (18 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.2192 (Rfree = 0.000) for 3817 atoms. Found 5 (18 requested) and removed 15 (9 requested) atoms. Cycle 25: After refmac, R = 0.2106 (Rfree = 0.000) for 3798 atoms. Found 3 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 3950 seeds are put forward Round 1: 231 peptides, 43 chains. Longest chain 10 peptides. Score 0.334 Round 2: 268 peptides, 45 chains. Longest chain 12 peptides. Score 0.405 Round 3: 270 peptides, 40 chains. Longest chain 18 peptides. Score 0.460 Round 4: 273 peptides, 39 chains. Longest chain 18 peptides. Score 0.477 Round 5: 267 peptides, 39 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 4 Chains 40, Residues 234, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8716 restraints for refining 3977 atoms. 7763 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2676 (Rfree = 0.000) for 3977 atoms. Found 18 (18 requested) and removed 48 (9 requested) atoms. Cycle 27: After refmac, R = 0.2316 (Rfree = 0.000) for 3921 atoms. Found 16 (18 requested) and removed 28 (9 requested) atoms. Cycle 28: After refmac, R = 0.2228 (Rfree = 0.000) for 3901 atoms. Found 10 (18 requested) and removed 23 (9 requested) atoms. Cycle 29: After refmac, R = 0.2185 (Rfree = 0.000) for 3883 atoms. Found 15 (18 requested) and removed 27 (9 requested) atoms. Cycle 30: After refmac, R = 0.2091 (Rfree = 0.000) for 3866 atoms. Found 9 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 4011 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4034 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 9 peptides. Score 0.320 Round 2: 247 peptides, 40 chains. Longest chain 15 peptides. Score 0.407 Round 3: 244 peptides, 40 chains. Longest chain 14 peptides. Score 0.399 Round 4: 247 peptides, 40 chains. Longest chain 15 peptides. Score 0.407 Round 5: 257 peptides, 40 chains. Longest chain 18 peptides. Score 0.430 Taking the results from Round 5 Chains 41, Residues 217, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9122 restraints for refining 4071 atoms. 8255 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2598 (Rfree = 0.000) for 4071 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 32: After refmac, R = 0.2337 (Rfree = 0.000) for 4015 atoms. Found 17 (19 requested) and removed 27 (9 requested) atoms. Cycle 33: After refmac, R = 0.2323 (Rfree = 0.000) for 3983 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 3968 atoms. Found 11 (18 requested) and removed 17 (9 requested) atoms. Cycle 35: After refmac, R = 0.2158 (Rfree = 0.000) for 3950 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 4065 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4080 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 12 peptides. Score 0.264 Round 2: 212 peptides, 38 chains. Longest chain 13 peptides. Score 0.341 Round 3: 217 peptides, 36 chains. Longest chain 13 peptides. Score 0.376 Round 4: 229 peptides, 37 chains. Longest chain 13 peptides. Score 0.395 Round 5: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 4 Chains 37, Residues 192, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9480 restraints for refining 4050 atoms. 8733 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2568 (Rfree = 0.000) for 4050 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 37: After refmac, R = 0.2465 (Rfree = 0.000) for 3995 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 38: After refmac, R = 0.2394 (Rfree = 0.000) for 3964 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 39: After refmac, R = 0.2559 (Rfree = 0.000) for 3936 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 40: After refmac, R = 0.2437 (Rfree = 0.000) for 3917 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 4070 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4085 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 11 peptides. Score 0.284 Round 2: 199 peptides, 33 chains. Longest chain 15 peptides. Score 0.364 Round 3: 200 peptides, 33 chains. Longest chain 13 peptides. Score 0.366 Round 4: 207 peptides, 33 chains. Longest chain 15 peptides. Score 0.384 Round 5: 202 peptides, 33 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 4 Chains 33, Residues 174, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9218 restraints for refining 4016 atoms. 8507 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2723 (Rfree = 0.000) for 4016 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 42: After refmac, R = 0.2426 (Rfree = 0.000) for 3966 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 43: After refmac, R = 0.1969 (Rfree = 0.000) for 3935 atoms. Found 7 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1847 (Rfree = 0.000) for 3920 atoms. Found 1 (18 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.1784 (Rfree = 0.000) for 3906 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 4018 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4034 seeds are put forward Round 1: 187 peptides, 36 chains. Longest chain 15 peptides. Score 0.296 Round 2: 213 peptides, 34 chains. Longest chain 14 peptides. Score 0.388 Round 3: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.378 Round 4: 196 peptides, 31 chains. Longest chain 17 peptides. Score 0.379 Round 5: 211 peptides, 35 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 179, 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 2ffj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5972 reflections ( 98.65 % complete ) and 8746 restraints for refining 3877 atoms. 8064 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2391 (Rfree = 0.000) for 3877 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2350 (Rfree = 0.000) for 3856 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 3835 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2363 (Rfree = 0.000) for 3810 atoms. TimeTaking 40.87