Mon 24 Dec 07:52:10 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 2f4p-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4p-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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/2f4p-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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 07:52:15 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/2f4p-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6456 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-4.0-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-4.0-parrot-noncs.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 4.001 Wilson plot Bfac: 75.05 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4616 reflections ( 99.29 % complete ) and 0 restraints for refining 5184 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3494 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3287 (Rfree = 0.000) for 5184 atoms. Found 24 (24 requested) and removed 82 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 5181 seeds are put forward NCS extension: 0 residues added, 5181 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 10 peptides. Score 0.244 Round 2: 185 peptides, 38 chains. Longest chain 8 peptides. Score 0.280 Round 3: 211 peptides, 40 chains. Longest chain 10 peptides. Score 0.336 Round 4: 232 peptides, 44 chains. Longest chain 13 peptides. Score 0.348 Round 5: 258 peptides, 43 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 5 Chains 43, Residues 215, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 10309 restraints for refining 4248 atoms. 9468 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2260 (Rfree = 0.000) for 4248 atoms. Found 17 (20 requested) and removed 51 (10 requested) atoms. Cycle 2: After refmac, R = 0.2138 (Rfree = 0.000) for 4136 atoms. Found 18 (20 requested) and removed 39 (10 requested) atoms. Cycle 3: After refmac, R = 0.2017 (Rfree = 0.000) for 4076 atoms. Found 11 (19 requested) and removed 20 (9 requested) atoms. Cycle 4: After refmac, R = 0.2061 (Rfree = 0.000) for 4032 atoms. Found 17 (19 requested) and removed 26 (9 requested) atoms. Cycle 5: After refmac, R = 0.2000 (Rfree = 0.000) for 3994 atoms. Found 16 (19 requested) and removed 33 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.86 Search for helices and strands: 0 residues in 0 chains, 4086 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 4116 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 9 peptides. Score 0.263 Round 2: 226 peptides, 42 chains. Longest chain 12 peptides. Score 0.355 Round 3: 240 peptides, 41 chains. Longest chain 11 peptides. Score 0.409 Round 4: 249 peptides, 41 chains. Longest chain 11 peptides. Score 0.434 Round 5: 255 peptides, 44 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 41, Residues 208, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 9183 restraints for refining 3957 atoms. 8374 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2094 (Rfree = 0.000) for 3957 atoms. Found 16 (18 requested) and removed 47 (9 requested) atoms. Cycle 7: After refmac, R = 0.1755 (Rfree = 0.000) for 3882 atoms. Found 10 (18 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.1822 (Rfree = 0.000) for 3848 atoms. Found 10 (18 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.1817 (Rfree = 0.000) for 3821 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.1934 (Rfree = 0.000) for 3806 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3919 seeds are put forward Round 1: 209 peptides, 44 chains. Longest chain 9 peptides. Score 0.277 Round 2: 229 peptides, 44 chains. Longest chain 12 peptides. Score 0.339 Round 3: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.399 Round 4: 242 peptides, 43 chains. Longest chain 12 peptides. Score 0.390 Round 5: 271 peptides, 48 chains. Longest chain 11 peptides. Score 0.411 Taking the results from Round 5 Chains 49, Residues 223, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8888 restraints for refining 3960 atoms. 7999 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2491 (Rfree = 0.000) for 3960 atoms. Found 18 (18 requested) and removed 53 (9 requested) atoms. Cycle 12: After refmac, R = 0.1950 (Rfree = 0.000) for 3871 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 13: After refmac, R = 0.1858 (Rfree = 0.000) for 3813 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 14: After refmac, R = 0.1811 (Rfree = 0.000) for 3786 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.1689 (Rfree = 0.000) for 3776 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3914 seeds are put forward Round 1: 177 peptides, 40 chains. Longest chain 7 peptides. Score 0.226 Round 2: 229 peptides, 41 chains. Longest chain 11 peptides. Score 0.377 Round 3: 227 peptides, 41 chains. Longest chain 16 peptides. Score 0.371 Round 4: 259 peptides, 44 chains. Longest chain 15 peptides. Score 0.426 Round 5: 254 peptides, 43 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 44, Residues 215, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8645 restraints for refining 3860 atoms. 7803 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2085 (Rfree = 0.000) for 3860 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 17: After refmac, R = 0.1710 (Rfree = 0.000) for 3795 atoms. Found 11 (18 requested) and removed 23 (9 requested) atoms. Cycle 18: After refmac, R = 0.1965 (Rfree = 0.000) for 3771 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.1480 (Rfree = 0.000) for 3756 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1566 (Rfree = 0.000) for 3748 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3904 seeds are put forward Round 1: 207 peptides, 44 chains. Longest chain 8 peptides. Score 0.271 Round 2: 228 peptides, 42 chains. Longest chain 15 peptides. Score 0.361 Round 3: 247 peptides, 43 chains. Longest chain 13 peptides. Score 0.404 Round 4: 253 peptides, 40 chains. Longest chain 17 peptides. Score 0.456 Round 5: 237 peptides, 41 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 4 Chains 40, Residues 213, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8471 restraints for refining 3826 atoms. 7638 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1760 (Rfree = 0.000) for 3826 atoms. Found 17 (18 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.1892 (Rfree = 0.000) for 3808 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 23: After refmac, R = 0.1655 (Rfree = 0.000) for 3789 atoms. Found 8 (18 requested) and removed 20 (9 requested) atoms. Cycle 24: After refmac, R = 0.1955 (Rfree = 0.000) for 3764 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 25: After refmac, R = 0.2208 (Rfree = 0.000) for 3747 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3895 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 8 peptides. Score 0.265 Round 2: 233 peptides, 40 chains. Longest chain 20 peptides. Score 0.401 Round 3: 218 peptides, 39 chains. Longest chain 12 peptides. Score 0.370 Round 4: 240 peptides, 40 chains. Longest chain 13 peptides. Score 0.421 Round 5: 242 peptides, 37 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 5 Chains 37, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8785 restraints for refining 3882 atoms. 8002 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2054 (Rfree = 0.000) for 3882 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 27: After refmac, R = 0.2341 (Rfree = 0.000) for 3826 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 28: After refmac, R = 0.1578 (Rfree = 0.000) for 3794 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.1499 (Rfree = 0.000) for 3788 atoms. Found 6 (18 requested) and removed 15 (9 requested) atoms. Cycle 30: After refmac, R = 0.1653 (Rfree = 0.000) for 3771 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.84 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3925 seeds are put forward Round 1: 156 peptides, 35 chains. Longest chain 7 peptides. Score 0.225 Round 2: 206 peptides, 40 chains. Longest chain 11 peptides. Score 0.320 Round 3: 235 peptides, 42 chains. Longest chain 14 peptides. Score 0.382 Round 4: 237 peptides, 43 chains. Longest chain 14 peptides. Score 0.375 Round 5: 241 peptides, 41 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 5 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8678 restraints for refining 3830 atoms. 7908 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1754 (Rfree = 0.000) for 3830 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 32: After refmac, R = 0.1546 (Rfree = 0.000) for 3811 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.1586 (Rfree = 0.000) for 3792 atoms. Found 17 (18 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 3786 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.1858 (Rfree = 0.000) for 3781 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3928 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 7 peptides. Score 0.249 Round 2: 193 peptides, 38 chains. Longest chain 10 peptides. Score 0.306 Round 3: 194 peptides, 35 chains. Longest chain 12 peptides. Score 0.349 Round 4: 187 peptides, 33 chains. Longest chain 12 peptides. Score 0.354 Round 5: 204 peptides, 34 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 34, Residues 170, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8916 restraints for refining 3919 atoms. 8232 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1659 (Rfree = 0.000) for 3919 atoms. Found 10 (18 requested) and removed 35 (9 requested) atoms. Cycle 37: After refmac, R = 0.1433 (Rfree = 0.000) for 3877 atoms. Found 6 (18 requested) and removed 20 (9 requested) atoms. Cycle 38: After refmac, R = 0.1320 (Rfree = 0.000) for 3841 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.1551 (Rfree = 0.000) for 3821 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1537 (Rfree = 0.000) for 3807 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 3932 seeds are put forward Round 1: 157 peptides, 35 chains. Longest chain 7 peptides. Score 0.228 Round 2: 181 peptides, 33 chains. Longest chain 11 peptides. Score 0.336 Round 3: 182 peptides, 33 chains. Longest chain 11 peptides. Score 0.339 Round 4: 194 peptides, 35 chains. Longest chain 11 peptides. Score 0.349 Round 5: 191 peptides, 36 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 4 Chains 35, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 9124 restraints for refining 3899 atoms. 8523 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1924 (Rfree = 0.000) for 3899 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 42: After refmac, R = 0.1749 (Rfree = 0.000) for 3856 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 43: After refmac, R = 0.1647 (Rfree = 0.000) for 3841 atoms. Found 15 (18 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.1379 (Rfree = 0.000) for 3827 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1405 (Rfree = 0.000) for 3823 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 3949 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3962 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 11 peptides. Score 0.227 Round 2: 184 peptides, 31 chains. Longest chain 11 peptides. Score 0.372 Round 3: 173 peptides, 31 chains. Longest chain 11 peptides. Score 0.338 Round 4: 164 peptides, 28 chains. Longest chain 12 peptides. Score 0.351 Round 5: 167 peptides, 28 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 153, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4616 reflections ( 99.29 % complete ) and 8385 restraints for refining 3724 atoms. 7804 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1842 (Rfree = 0.000) for 3724 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1578 (Rfree = 0.000) for 3707 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1590 (Rfree = 0.000) for 3696 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1420 (Rfree = 0.000) for 3686 atoms. TimeTaking 47.7