Sun 23 Dec 22:22:53 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 2pke-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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/2pke-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 22:23:03 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/2pke-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.4-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 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-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.4-parrot-hancs.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 4423 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3005 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2669 (Rfree = 0.000) for 4423 atoms. Found 33 (33 requested) and removed 60 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 4507 seeds are put forward NCS extension: 0 residues added, 4507 seeds are put forward Round 1: 177 peptides, 36 chains. Longest chain 9 peptides. Score 0.302 Round 2: 243 peptides, 40 chains. Longest chain 17 peptides. Score 0.475 Round 3: 243 peptides, 38 chains. Longest chain 12 peptides. Score 0.502 Round 4: 249 peptides, 38 chains. Longest chain 14 peptides. Score 0.521 Round 5: 246 peptides, 38 chains. Longest chain 15 peptides. Score 0.511 Taking the results from Round 4 Chains 39, Residues 211, Estimated correctness of the model 0.8 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8543 restraints for refining 3651 atoms. 7670 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2124 (Rfree = 0.000) for 3651 atoms. Found 18 (27 requested) and removed 39 (13 requested) atoms. Cycle 2: After refmac, R = 0.1981 (Rfree = 0.000) for 3592 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. Cycle 3: After refmac, R = 0.1941 (Rfree = 0.000) for 3568 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.1928 (Rfree = 0.000) for 3550 atoms. Found 4 (26 requested) and removed 19 (13 requested) atoms. Cycle 5: After refmac, R = 0.1915 (Rfree = 0.000) for 3534 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 3677 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3692 seeds are put forward Round 1: 217 peptides, 43 chains. Longest chain 12 peptides. Score 0.343 Round 2: 241 peptides, 41 chains. Longest chain 16 peptides. Score 0.455 Round 3: 251 peptides, 40 chains. Longest chain 15 peptides. Score 0.500 Round 4: 254 peptides, 37 chains. Longest chain 19 peptides. Score 0.548 Round 5: 246 peptides, 36 chains. Longest chain 16 peptides. Score 0.538 Taking the results from Round 4 Chains 37, Residues 217, Estimated correctness of the model 10.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8255 restraints for refining 3566 atoms. 7397 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2159 (Rfree = 0.000) for 3566 atoms. Found 13 (26 requested) and removed 48 (13 requested) atoms. Cycle 7: After refmac, R = 0.2023 (Rfree = 0.000) for 3520 atoms. Found 14 (26 requested) and removed 18 (13 requested) atoms. Cycle 8: After refmac, R = 0.1962 (Rfree = 0.000) for 3508 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.1935 (Rfree = 0.000) for 3491 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.1918 (Rfree = 0.000) for 3477 atoms. Found 2 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3626 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 12 peptides. Score 0.399 Round 2: 239 peptides, 39 chains. Longest chain 13 peptides. Score 0.476 Round 3: 249 peptides, 39 chains. Longest chain 14 peptides. Score 0.507 Round 4: 256 peptides, 40 chains. Longest chain 13 peptides. Score 0.515 Round 5: 246 peptides, 40 chains. Longest chain 13 peptides. Score 0.485 Taking the results from Round 4 Chains 42, Residues 216, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8107 restraints for refining 3531 atoms. 7171 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2161 (Rfree = 0.000) for 3531 atoms. Found 17 (26 requested) and removed 35 (13 requested) atoms. Cycle 12: After refmac, R = 0.2026 (Rfree = 0.000) for 3506 atoms. Found 10 (26 requested) and removed 16 (13 requested) atoms. Cycle 13: After refmac, R = 0.2013 (Rfree = 0.000) for 3498 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 14: After refmac, R = 0.2021 (Rfree = 0.000) for 3486 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.2015 (Rfree = 0.000) for 3479 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3649 seeds are put forward Round 1: 202 peptides, 41 chains. Longest chain 12 peptides. Score 0.318 Round 2: 228 peptides, 39 chains. Longest chain 13 peptides. Score 0.440 Round 3: 241 peptides, 39 chains. Longest chain 15 peptides. Score 0.483 Round 4: 230 peptides, 37 chains. Longest chain 19 peptides. Score 0.475 Round 5: 244 peptides, 39 chains. Longest chain 17 peptides. Score 0.492 Taking the results from Round 5 Chains 41, Residues 205, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8439 restraints for refining 3600 atoms. 7608 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2309 (Rfree = 0.000) for 3600 atoms. Found 13 (27 requested) and removed 23 (13 requested) atoms. Cycle 17: After refmac, R = 0.2218 (Rfree = 0.000) for 3576 atoms. Found 10 (27 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.2186 (Rfree = 0.000) for 3565 atoms. Found 8 (26 requested) and removed 19 (13 requested) atoms. Cycle 19: After refmac, R = 0.2206 (Rfree = 0.000) for 3551 atoms. Found 11 (26 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2212 (Rfree = 0.000) for 3545 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 3697 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3715 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 8 peptides. Score 0.318 Round 2: 201 peptides, 35 chains. Longest chain 12 peptides. Score 0.407 Round 3: 213 peptides, 33 chains. Longest chain 12 peptides. Score 0.476 Round 4: 205 peptides, 32 chains. Longest chain 15 peptides. Score 0.464 Round 5: 204 peptides, 31 chains. Longest chain 12 peptides. Score 0.475 Taking the results from Round 3 Chains 33, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8724 restraints for refining 3601 atoms. 8037 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2190 (Rfree = 0.000) for 3601 atoms. Found 13 (27 requested) and removed 22 (13 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 3584 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2093 (Rfree = 0.000) for 3571 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2114 (Rfree = 0.000) for 3565 atoms. Found 18 (26 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2085 (Rfree = 0.000) for 3567 atoms. Found 14 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3732 seeds are put forward Round 1: 196 peptides, 35 chains. Longest chain 15 peptides. Score 0.389 Round 2: 208 peptides, 32 chains. Longest chain 16 peptides. Score 0.474 Round 3: 208 peptides, 31 chains. Longest chain 17 peptides. Score 0.488 Round 4: 217 peptides, 30 chains. Longest chain 18 peptides. Score 0.530 Round 5: 219 peptides, 31 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 4 Chains 31, Residues 187, Estimated correctness of the model 4.2 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8538 restraints for refining 3651 atoms. 7746 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2233 (Rfree = 0.000) for 3651 atoms. Found 14 (27 requested) and removed 23 (13 requested) atoms. Cycle 27: After refmac, R = 0.2154 (Rfree = 0.000) for 3631 atoms. Found 6 (27 requested) and removed 17 (13 requested) atoms. Cycle 28: After refmac, R = 0.2157 (Rfree = 0.000) for 3612 atoms. Found 17 (27 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.2097 (Rfree = 0.000) for 3615 atoms. Found 15 (27 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2000 (Rfree = 0.000) for 3610 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 3759 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3772 seeds are put forward Round 1: 158 peptides, 29 chains. Longest chain 14 peptides. Score 0.343 Round 2: 186 peptides, 33 chains. Longest chain 14 peptides. Score 0.384 Round 3: 205 peptides, 31 chains. Longest chain 14 peptides. Score 0.479 Round 4: 189 peptides, 30 chains. Longest chain 14 peptides. Score 0.440 Round 5: 195 peptides, 32 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 3 Chains 31, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8684 restraints for refining 3612 atoms. 8019 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2049 (Rfree = 0.000) for 3612 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. Cycle 32: After refmac, R = 0.2012 (Rfree = 0.000) for 3596 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. Cycle 33: After refmac, R = 0.2051 (Rfree = 0.000) for 3581 atoms. Found 14 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.2026 (Rfree = 0.000) for 3575 atoms. Found 9 (27 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = (Rfree = 0.000) for 3566 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 3670 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3689 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 9 peptides. Score 0.293 Round 2: 187 peptides, 30 chains. Longest chain 14 peptides. Score 0.433 Round 3: 193 peptides, 31 chains. Longest chain 12 peptides. Score 0.439 Round 4: 192 peptides, 28 chains. Longest chain 19 peptides. Score 0.479 Round 5: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 4 Chains 28, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8995 restraints for refining 3607 atoms. 8367 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 3607 atoms. Found 12 (27 requested) and removed 17 (13 requested) atoms. Cycle 37: After refmac, R = 0.2029 (Rfree = 0.000) for 3594 atoms. Found 6 (27 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2057 (Rfree = 0.000) for 3586 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2012 (Rfree = 0.000) for 3574 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1996 (Rfree = 0.000) for 3563 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 3697 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3724 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 12 peptides. Score 0.329 Round 2: 180 peptides, 30 chains. Longest chain 15 peptides. Score 0.408 Round 3: 174 peptides, 29 chains. Longest chain 12 peptides. Score 0.403 Round 4: 181 peptides, 27 chains. Longest chain 19 peptides. Score 0.458 Round 5: 187 peptides, 29 chains. Longest chain 20 peptides. Score 0.448 Taking the results from Round 4 Chains 28, Residues 154, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5889 reflections ( 96.32 % complete ) and 8562 restraints for refining 3566 atoms. 7945 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1955 (Rfree = 0.000) for 3566 atoms. Found 10 (26 requested) and removed 19 (13 requested) atoms. Cycle 42: After refmac, R = 0.2109 (Rfree = 0.000) for 3553 atoms. Found 24 (26 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.1932 (Rfree = 0.000) for 3557 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.1797 (Rfree = 0.000) for 3549 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1958 (Rfree = 0.000) for 3541 atoms. Found 21 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 3694 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3713 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 9 peptides. Score 0.284 Round 2: 165 peptides, 25 chains. Longest chain 18 peptides. Score 0.433 Round 3: 160 peptides, 25 chains. Longest chain 21 peptides. Score 0.415 Round 4: 156 peptides, 25 chains. Longest chain 15 peptides. Score 0.401 Round 5: 164 peptides, 26 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 140, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (140 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5889 reflections ( 96.32 % complete ) and 8730 restraints for refining 3593 atoms. 8169 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1890 (Rfree = 0.000) for 3593 atoms. Found 0 (27 requested) and removed 8 (13 requested) atoms. Cycle 47: After refmac, R = 0.1767 (Rfree = 0.000) for 3583 atoms. Found 0 (27 requested) and removed 2 (13 requested) atoms. Cycle 48: After refmac, R = 0.1753 (Rfree = 0.000) for 3580 atoms. Found 0 (27 requested) and removed 3 (13 requested) atoms. Cycle 49: After refmac, R = 0.1735 (Rfree = 0.000) for 3576 atoms. TimeTaking 54.87