Mon 24 Dec 08:04:51 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 2pke-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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/2pke-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 08:04:56 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/2pke-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 298 and 0 Target number of residues in the AU: 298 Target solvent content: 0.6412 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.4-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.400 Wilson plot Bfac: 72.66 5889 reflections ( 96.32 % complete ) and 0 restraints for refining 4456 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3044 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2982 (Rfree = 0.000) for 4456 atoms. Found 33 (33 requested) and removed 84 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 4509 seeds are put forward NCS extension: 0 residues added, 4509 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.281 Round 2: 200 peptides, 38 chains. Longest chain 13 peptides. Score 0.357 Round 3: 221 peptides, 37 chains. Longest chain 12 peptides. Score 0.446 Round 4: 226 peptides, 36 chains. Longest chain 15 peptides. Score 0.476 Round 5: 229 peptides, 34 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 5 Chains 37, Residues 195, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8480 restraints for refining 3652 atoms. 7644 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2540 (Rfree = 0.000) for 3652 atoms. Found 24 (27 requested) and removed 42 (13 requested) atoms. Cycle 2: After refmac, R = 0.2330 (Rfree = 0.000) for 3592 atoms. Found 27 (27 requested) and removed 141 (13 requested) atoms. Cycle 3: After refmac, R = 0.2190 (Rfree = 0.000) for 3462 atoms. Found 13 (26 requested) and removed 49 (13 requested) atoms. Cycle 4: After refmac, R = 0.2119 (Rfree = 0.000) for 3414 atoms. Found 5 (25 requested) and removed 29 (12 requested) atoms. Cycle 5: After refmac, R = 0.2119 (Rfree = 0.000) for 3383 atoms. Found 7 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3530 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 8 peptides. Score 0.246 Round 2: 203 peptides, 39 chains. Longest chain 9 peptides. Score 0.353 Round 3: 224 peptides, 40 chains. Longest chain 11 peptides. Score 0.412 Round 4: 217 peptides, 39 chains. Longest chain 11 peptides. Score 0.403 Round 5: 205 peptides, 37 chains. Longest chain 10 peptides. Score 0.390 Taking the results from Round 3 Chains 40, Residues 184, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8132 restraints for refining 3524 atoms. 7363 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2259 (Rfree = 0.000) for 3524 atoms. Found 24 (26 requested) and removed 58 (13 requested) atoms. Cycle 7: After refmac, R = 0.2173 (Rfree = 0.000) for 3472 atoms. Found 11 (26 requested) and removed 43 (13 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 3436 atoms. Found 16 (25 requested) and removed 57 (12 requested) atoms. Cycle 9: After refmac, R = 0.2186 (Rfree = 0.000) for 3394 atoms. Found 6 (25 requested) and removed 27 (12 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 3372 atoms. Found 12 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3511 seeds are put forward Round 1: 175 peptides, 39 chains. Longest chain 8 peptides. Score 0.245 Round 2: 203 peptides, 39 chains. Longest chain 8 peptides. Score 0.353 Round 3: 207 peptides, 39 chains. Longest chain 10 peptides. Score 0.367 Round 4: 205 peptides, 39 chains. Longest chain 9 peptides. Score 0.360 Round 5: 204 peptides, 37 chains. Longest chain 10 peptides. Score 0.387 Taking the results from Round 5 Chains 37, Residues 167, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8472 restraints for refining 3596 atoms. 7810 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2293 (Rfree = 0.000) for 3596 atoms. Found 19 (27 requested) and removed 55 (13 requested) atoms. Cycle 12: After refmac, R = 0.2125 (Rfree = 0.000) for 3553 atoms. Found 15 (26 requested) and removed 25 (13 requested) atoms. Cycle 13: After refmac, R = 0.2057 (Rfree = 0.000) for 3541 atoms. Found 12 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2070 (Rfree = 0.000) for 3527 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.2060 (Rfree = 0.000) for 3519 atoms. Found 14 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 3654 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3666 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 8 peptides. Score 0.274 Round 2: 188 peptides, 34 chains. Longest chain 9 peptides. Score 0.375 Round 3: 191 peptides, 33 chains. Longest chain 10 peptides. Score 0.401 Round 4: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.386 Round 5: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 34, Residues 168, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8339 restraints for refining 3652 atoms. 7599 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2445 (Rfree = 0.000) for 3652 atoms. Found 19 (27 requested) and removed 42 (13 requested) atoms. Cycle 17: After refmac, R = 0.2230 (Rfree = 0.000) for 3622 atoms. Found 8 (27 requested) and removed 21 (13 requested) atoms. Cycle 18: After refmac, R = 0.2139 (Rfree = 0.000) for 3605 atoms. Found 5 (27 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2210 (Rfree = 0.000) for 3590 atoms. Found 24 (27 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2028 (Rfree = 0.000) for 3600 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3739 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 9 peptides. Score 0.275 Round 2: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.381 Round 3: 175 peptides, 30 chains. Longest chain 10 peptides. Score 0.391 Round 4: 172 peptides, 28 chains. Longest chain 11 peptides. Score 0.411 Round 5: 169 peptides, 28 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 4 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8386 restraints for refining 3652 atoms. 7756 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2219 (Rfree = 0.000) for 3652 atoms. Found 20 (27 requested) and removed 22 (13 requested) atoms. Cycle 22: After refmac, R = 0.2067 (Rfree = 0.000) for 3646 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2071 (Rfree = 0.000) for 3639 atoms. Found 20 (27 requested) and removed 23 (13 requested) atoms. Cycle 24: After refmac, R = 0.2035 (Rfree = 0.000) for 3634 atoms. Found 15 (27 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2028 (Rfree = 0.000) for 3630 atoms. Found 7 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 3736 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3746 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 8 peptides. Score 0.284 Round 2: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.386 Round 3: 178 peptides, 31 chains. Longest chain 14 peptides. Score 0.386 Round 4: 175 peptides, 30 chains. Longest chain 13 peptides. Score 0.391 Round 5: 176 peptides, 31 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 31, Residues 145, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8323 restraints for refining 3652 atoms. 7699 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2396 (Rfree = 0.000) for 3652 atoms. Found 24 (27 requested) and removed 28 (13 requested) atoms. Cycle 27: After refmac, R = 0.2191 (Rfree = 0.000) for 3643 atoms. Found 19 (27 requested) and removed 25 (13 requested) atoms. Cycle 28: After refmac, R = 0.2082 (Rfree = 0.000) for 3634 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. Cycle 29: After refmac, R = 0.2046 (Rfree = 0.000) for 3623 atoms. Found 5 (27 requested) and removed 17 (13 requested) atoms. Cycle 30: After refmac, R = 0.2043 (Rfree = 0.000) for 3608 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3724 seeds are put forward Round 1: 150 peptides, 31 chains. Longest chain 8 peptides. Score 0.278 Round 2: 175 peptides, 33 chains. Longest chain 11 peptides. Score 0.343 Round 3: 169 peptides, 29 chains. Longest chain 13 peptides. Score 0.384 Round 4: 154 peptides, 26 chains. Longest chain 14 peptides. Score 0.377 Round 5: 167 peptides, 28 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 28, Residues 139, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8454 restraints for refining 3652 atoms. 7867 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2266 (Rfree = 0.000) for 3652 atoms. Found 20 (27 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.2089 (Rfree = 0.000) for 3650 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 33: After refmac, R = 0.2013 (Rfree = 0.000) for 3642 atoms. Found 12 (27 requested) and removed 16 (13 requested) atoms. Cycle 34: After refmac, R = 0.2012 (Rfree = 0.000) for 3634 atoms. Found 13 (27 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.2012 (Rfree = 0.000) for 3630 atoms. Found 21 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.70 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3744 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 10 peptides. Score 0.270 Round 2: 167 peptides, 31 chains. Longest chain 11 peptides. Score 0.345 Round 3: 170 peptides, 29 chains. Longest chain 12 peptides. Score 0.388 Round 4: 176 peptides, 30 chains. Longest chain 10 peptides. Score 0.394 Round 5: 189 peptides, 30 chains. Longest chain 11 peptides. Score 0.440 Taking the results from Round 5 Chains 30, Residues 159, Estimated correctness of the model 0.0 % 7 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8082 restraints for refining 3652 atoms. 7352 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2228 (Rfree = 0.000) for 3652 atoms. Found 18 (27 requested) and removed 33 (13 requested) atoms. Cycle 37: After refmac, R = 0.2254 (Rfree = 0.000) for 3629 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2131 (Rfree = 0.000) for 3629 atoms. Found 23 (27 requested) and removed 15 (13 requested) atoms. Cycle 39: After refmac, R = 0.2051 (Rfree = 0.000) for 3633 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 40: After refmac, R = 0.2230 (Rfree = 0.000) for 3625 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.53 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3736 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 10 peptides. Score 0.233 Round 2: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.326 Round 3: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.326 Round 4: 164 peptides, 31 chains. Longest chain 10 peptides. Score 0.333 Round 5: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Chains 30, Residues 133, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8486 restraints for refining 3652 atoms. 7932 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2330 (Rfree = 0.000) for 3652 atoms. Found 19 (27 requested) and removed 27 (13 requested) atoms. Cycle 42: After refmac, R = 0.2205 (Rfree = 0.000) for 3640 atoms. Found 26 (27 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2703 (Rfree = 0.000) for 3643 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 44: After refmac, R = 0.2284 (Rfree = 0.000) for 3632 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 45: After refmac, R = 0.2124 (Rfree = 0.000) for 3630 atoms. Found 16 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.62 Search for helices and strands: 0 residues in 0 chains, 3735 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3740 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.258 Round 2: 126 peptides, 24 chains. Longest chain 8 peptides. Score 0.301 Round 3: 128 peptides, 23 chains. Longest chain 8 peptides. Score 0.327 Round 4: 132 peptides, 24 chains. Longest chain 8 peptides. Score 0.326 Round 5: 144 peptides, 27 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 105, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 204 A and 218 A 21 chains (114 residues) following loop building 2 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5889 reflections ( 96.32 % complete ) and 8474 restraints for refining 3648 atoms. 7949 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2371 (Rfree = 0.000) for 3648 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2336 (Rfree = 0.000) for 3626 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2963 (Rfree = 0.000) for 3610 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2520 (Rfree = 0.000) for 3594 atoms. TimeTaking 35.82