Sun 23 Dec 23:52:01 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 2pke-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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/2pke-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 ============================================================ Sun 23 Dec 23:52:05 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/2pke-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 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-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.4-parrot-mrncs.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 4458 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.2968 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2661 (Rfree = 0.000) for 4458 atoms. Found 33 (33 requested) and removed 58 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 4550 seeds are put forward NCS extension: 0 residues added, 4550 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.297 Round 2: 232 peptides, 40 chains. Longest chain 15 peptides. Score 0.439 Round 3: 249 peptides, 42 chains. Longest chain 15 peptides. Score 0.467 Round 4: 251 peptides, 36 chains. Longest chain 23 peptides. Score 0.552 Round 5: 258 peptides, 37 chains. Longest chain 23 peptides. Score 0.559 Taking the results from Round 5 Chains 40, Residues 221, Estimated correctness of the model 14.7 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8378 restraints for refining 3650 atoms. 7444 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2179 (Rfree = 0.000) for 3650 atoms. Found 21 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2004 (Rfree = 0.000) for 3596 atoms. Found 20 (27 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.1855 (Rfree = 0.000) for 3576 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.1817 (Rfree = 0.000) for 3558 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2055 (Rfree = 0.000) for 3540 atoms. Found 25 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3723 seeds are put forward Round 1: 195 peptides, 37 chains. Longest chain 11 peptides. Score 0.354 Round 2: 249 peptides, 40 chains. Longest chain 14 peptides. Score 0.494 Round 3: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.547 Round 4: 255 peptides, 36 chains. Longest chain 16 peptides. Score 0.563 Round 5: 246 peptides, 36 chains. Longest chain 17 peptides. Score 0.538 Taking the results from Round 4 Chains 37, Residues 219, Estimated correctness of the model 16.1 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8103 restraints for refining 3629 atoms. 7108 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2141 (Rfree = 0.000) for 3629 atoms. Found 23 (27 requested) and removed 57 (13 requested) atoms. Cycle 7: After refmac, R = 0.2035 (Rfree = 0.000) for 3578 atoms. Found 21 (27 requested) and removed 29 (13 requested) atoms. Cycle 8: After refmac, R = 0.2038 (Rfree = 0.000) for 3563 atoms. Found 12 (26 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.2017 (Rfree = 0.000) for 3554 atoms. Found 14 (26 requested) and removed 17 (13 requested) atoms. Cycle 10: After refmac, R = 0.2010 (Rfree = 0.000) for 3550 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 3683 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3699 seeds are put forward Round 1: 212 peptides, 39 chains. Longest chain 16 peptides. Score 0.385 Round 2: 224 peptides, 37 chains. Longest chain 16 peptides. Score 0.455 Round 3: 224 peptides, 34 chains. Longest chain 23 peptides. Score 0.497 Round 4: 233 peptides, 35 chains. Longest chain 16 peptides. Score 0.512 Round 5: 239 peptides, 36 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 5 Chains 36, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8859 restraints for refining 3643 atoms. 8083 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 3643 atoms. Found 17 (27 requested) and removed 40 (13 requested) atoms. Cycle 12: After refmac, R = 0.2518 (Rfree = 0.000) for 3611 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.2039 (Rfree = 0.000) for 3595 atoms. Found 17 (27 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.2020 (Rfree = 0.000) for 3592 atoms. Found 5 (27 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.2013 (Rfree = 0.000) for 3583 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 3727 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3745 seeds are put forward Round 1: 199 peptides, 37 chains. Longest chain 13 peptides. Score 0.369 Round 2: 214 peptides, 33 chains. Longest chain 14 peptides. Score 0.479 Round 3: 212 peptides, 31 chains. Longest chain 15 peptides. Score 0.501 Round 4: 210 peptides, 32 chains. Longest chain 15 peptides. Score 0.481 Round 5: 222 peptides, 32 chains. Longest chain 17 peptides. Score 0.518 Taking the results from Round 5 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8704 restraints for refining 3650 atoms. 7940 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2102 (Rfree = 0.000) for 3650 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 17: After refmac, R = 0.2038 (Rfree = 0.000) for 3646 atoms. Found 23 (27 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.1972 (Rfree = 0.000) for 3645 atoms. Found 18 (27 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.1976 (Rfree = 0.000) for 3648 atoms. Found 6 (27 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 3639 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 3792 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3804 seeds are put forward Round 1: 176 peptides, 33 chains. Longest chain 11 peptides. Score 0.347 Round 2: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.405 Round 3: 219 peptides, 32 chains. Longest chain 17 peptides. Score 0.509 Round 4: 216 peptides, 34 chains. Longest chain 20 peptides. Score 0.472 Round 5: 214 peptides, 35 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 3 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8596 restraints for refining 3652 atoms. 7808 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2060 (Rfree = 0.000) for 3652 atoms. Found 18 (27 requested) and removed 42 (13 requested) atoms. Cycle 22: After refmac, R = 0.2550 (Rfree = 0.000) for 3621 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 23: After refmac, R = 0.2604 (Rfree = 0.000) for 3600 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 24: After refmac, R = 0.2199 (Rfree = 0.000) for 3588 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 25: After refmac, R = 0.1748 (Rfree = 0.000) for 3585 atoms. Found 20 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.70 Search for helices and strands: 0 residues in 0 chains, 3731 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3747 seeds are put forward Round 1: 178 peptides, 38 chains. Longest chain 11 peptides. Score 0.274 Round 2: 192 peptides, 32 chains. Longest chain 12 peptides. Score 0.420 Round 3: 189 peptides, 33 chains. Longest chain 11 peptides. Score 0.394 Round 4: 191 peptides, 31 chains. Longest chain 18 peptides. Score 0.432 Round 5: 170 peptides, 28 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 4 Chains 31, Residues 160, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8661 restraints for refining 3639 atoms. 8014 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1838 (Rfree = 0.000) for 3639 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 27: After refmac, R = 0.1917 (Rfree = 0.000) for 3640 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 28: After refmac, R = 0.2145 (Rfree = 0.000) for 3640 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 29: After refmac, R = 0.1748 (Rfree = 0.000) for 3635 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.1783 (Rfree = 0.000) for 3642 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 3783 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3808 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 17 peptides. Score 0.308 Round 2: 199 peptides, 36 chains. Longest chain 18 peptides. Score 0.384 Round 3: 199 peptides, 32 chains. Longest chain 18 peptides. Score 0.444 Round 4: 188 peptides, 31 chains. Longest chain 12 peptides. Score 0.421 Round 5: 181 peptides, 31 chains. Longest chain 18 peptides. Score 0.397 Taking the results from Round 3 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8696 restraints for refining 3652 atoms. 8026 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1856 (Rfree = 0.000) for 3652 atoms. Found 21 (27 requested) and removed 21 (13 requested) atoms. Cycle 32: After refmac, R = 0.1679 (Rfree = 0.000) for 3644 atoms. Found 15 (27 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.1817 (Rfree = 0.000) for 3639 atoms. Found 23 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.1756 (Rfree = 0.000) for 3643 atoms. Found 20 (27 requested) and removed 19 (13 requested) atoms. Cycle 35: After refmac, R = 0.2772 (Rfree = 0.000) for 3641 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 3786 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 3821 seeds are put forward Round 1: 157 peptides, 31 chains. Longest chain 18 peptides. Score 0.306 Round 2: 175 peptides, 32 chains. Longest chain 12 peptides. Score 0.359 Round 3: 182 peptides, 31 chains. Longest chain 13 peptides. Score 0.400 Round 4: 188 peptides, 33 chains. Longest chain 13 peptides. Score 0.391 Round 5: 180 peptides, 32 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 3 Chains 31, Residues 151, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8873 restraints for refining 3652 atoms. 8281 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1834 (Rfree = 0.000) for 3652 atoms. Found 25 (27 requested) and removed 27 (13 requested) atoms. Cycle 37: After refmac, R = 0.1889 (Rfree = 0.000) for 3641 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.2142 (Rfree = 0.000) for 3639 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.1531 (Rfree = 0.000) for 3634 atoms. Found 15 (27 requested) and removed 15 (13 requested) atoms. Cycle 40: After refmac, R = 0.1451 (Rfree = 0.000) for 3628 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 3769 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3783 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 7 peptides. Score 0.241 Round 2: 171 peptides, 30 chains. Longest chain 18 peptides. Score 0.376 Round 3: 171 peptides, 27 chains. Longest chain 10 peptides. Score 0.423 Round 4: 179 peptides, 26 chains. Longest chain 19 peptides. Score 0.466 Round 5: 176 peptides, 28 chains. Longest chain 9 peptides. Score 0.425 Taking the results from Round 4 Chains 26, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8669 restraints for refining 3591 atoms. 8083 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1888 (Rfree = 0.000) for 3591 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 42: After refmac, R = 0.2050 (Rfree = 0.000) for 3586 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 43: After refmac, R = 0.1945 (Rfree = 0.000) for 3581 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 44: After refmac, R = 0.1498 (Rfree = 0.000) for 3585 atoms. Found 15 (27 requested) and removed 15 (13 requested) atoms. Cycle 45: After refmac, R = 0.1403 (Rfree = 0.000) for 3584 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3732 seeds are put forward Round 1: 140 peptides, 30 chains. Longest chain 8 peptides. Score 0.254 Round 2: 168 peptides, 32 chains. Longest chain 8 peptides. Score 0.332 Round 3: 162 peptides, 26 chains. Longest chain 17 peptides. Score 0.407 Round 4: 147 peptides, 27 chains. Longest chain 8 peptides. Score 0.334 Round 5: 147 peptides, 26 chains. Longest chain 8 peptides. Score 0.351 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 136, 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 2pke-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5889 reflections ( 96.32 % complete ) and 8459 restraints for refining 3513 atoms. 7941 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1612 (Rfree = 0.000) for 3513 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1519 (Rfree = 0.000) for 3494 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1543 (Rfree = 0.000) for 3480 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1525 (Rfree = 0.000) for 3467 atoms. TimeTaking 38.37