null Sun 23 Dec 22:23:02 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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 22:23:12 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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 291 and 0 Target number of residues in the AU: 291 Target solvent content: 0.6496 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 77.87 4971 reflections ( 96.02 % complete ) and 0 restraints for refining 4455 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3016 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2793 (Rfree = 0.000) for 4455 atoms. Found 28 (28 requested) and removed 58 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 4.02 Search for helices and strands: 0 residues in 0 chains, 4525 seeds are put forward NCS extension: 0 residues added, 4525 seeds are put forward Round 1: 183 peptides, 37 chains. Longest chain 15 peptides. Score 0.309 Round 2: 246 peptides, 42 chains. Longest chain 19 peptides. Score 0.457 Round 3: 247 peptides, 39 chains. Longest chain 19 peptides. Score 0.501 Round 4: 247 peptides, 33 chains. Longest chain 19 peptides. Score 0.578 Round 5: 260 peptides, 32 chains. Longest chain 21 peptides. Score 0.624 Taking the results from Round 5 Chains 32, Residues 228, Estimated correctness of the model 23.8 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8133 restraints for refining 3641 atoms. 7117 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2233 (Rfree = 0.000) for 3641 atoms. Found 16 (23 requested) and removed 35 (11 requested) atoms. Cycle 2: After refmac, R = 0.2225 (Rfree = 0.000) for 3573 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 3: After refmac, R = 0.2042 (Rfree = 0.000) for 3543 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 4: After refmac, R = 0.2047 (Rfree = 0.000) for 3519 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 5: After refmac, R = 0.1647 (Rfree = 0.000) for 3513 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 3667 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3693 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 12 peptides. Score 0.345 Round 2: 247 peptides, 40 chains. Longest chain 14 peptides. Score 0.488 Round 3: 252 peptides, 35 chains. Longest chain 17 peptides. Score 0.567 Round 4: 262 peptides, 39 chains. Longest chain 21 peptides. Score 0.546 Round 5: 256 peptides, 37 chains. Longest chain 16 peptides. Score 0.554 Taking the results from Round 3 Chains 37, Residues 217, Estimated correctness of the model 1.3 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8066 restraints for refining 3575 atoms. 7107 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2030 (Rfree = 0.000) for 3575 atoms. Found 22 (22 requested) and removed 42 (11 requested) atoms. Cycle 7: After refmac, R = 0.1963 (Rfree = 0.000) for 3537 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 8: After refmac, R = 0.1883 (Rfree = 0.000) for 3528 atoms. Found 12 (22 requested) and removed 19 (11 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 3509 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 10: After refmac, R = 0.1731 (Rfree = 0.000) for 3501 atoms. Found 19 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 3643 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3656 seeds are put forward Round 1: 207 peptides, 33 chains. Longest chain 14 peptides. Score 0.457 Round 2: 245 peptides, 37 chains. Longest chain 14 peptides. Score 0.522 Round 3: 246 peptides, 34 chains. Longest chain 19 peptides. Score 0.563 Round 4: 240 peptides, 33 chains. Longest chain 22 peptides. Score 0.558 Round 5: 235 peptides, 34 chains. Longest chain 22 peptides. Score 0.531 Taking the results from Round 3 Chains 36, Residues 212, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8120 restraints for refining 3558 atoms. 7245 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1930 (Rfree = 0.000) for 3558 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 12: After refmac, R = 0.1903 (Rfree = 0.000) for 3531 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 13: After refmac, R = 0.1878 (Rfree = 0.000) for 3523 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 14: After refmac, R = 0.1755 (Rfree = 0.000) for 3516 atoms. Found 22 (22 requested) and removed 71 (11 requested) atoms. Cycle 15: After refmac, R = 0.1481 (Rfree = 0.000) for 3462 atoms. Found 14 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.91 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3625 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 9 peptides. Score 0.324 Round 2: 214 peptides, 35 chains. Longest chain 15 peptides. Score 0.451 Round 3: 219 peptides, 35 chains. Longest chain 14 peptides. Score 0.467 Round 4: 218 peptides, 32 chains. Longest chain 19 peptides. Score 0.506 Round 5: 226 peptides, 37 chains. Longest chain 16 peptides. Score 0.462 Taking the results from Round 4 Chains 33, Residues 186, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8301 restraints for refining 3553 atoms. 7530 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1901 (Rfree = 0.000) for 3553 atoms. Found 12 (22 requested) and removed 39 (11 requested) atoms. Cycle 17: After refmac, R = 0.1855 (Rfree = 0.000) for 3517 atoms. Found 18 (22 requested) and removed 21 (11 requested) atoms. Cycle 18: After refmac, R = 0.1599 (Rfree = 0.000) for 3511 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. Cycle 19: After refmac, R = 0.1556 (Rfree = 0.000) for 3497 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 20: After refmac, R = 0.1522 (Rfree = 0.000) for 3486 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 3625 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3643 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 12 peptides. Score 0.346 Round 2: 206 peptides, 32 chains. Longest chain 16 peptides. Score 0.468 Round 3: 222 peptides, 35 chains. Longest chain 15 peptides. Score 0.477 Round 4: 221 peptides, 31 chains. Longest chain 15 peptides. Score 0.529 Round 5: 231 peptides, 33 chains. Longest chain 17 peptides. Score 0.532 Taking the results from Round 5 Chains 33, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8538 restraints for refining 3563 atoms. 7779 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2005 (Rfree = 0.000) for 3563 atoms. Found 22 (22 requested) and removed 53 (11 requested) atoms. Cycle 22: After refmac, R = 0.1767 (Rfree = 0.000) for 3523 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 23: After refmac, R = 0.1805 (Rfree = 0.000) for 3518 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 24: After refmac, R = 0.1674 (Rfree = 0.000) for 3520 atoms. Found 18 (22 requested) and removed 21 (11 requested) atoms. Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 3515 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 3675 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3709 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 9 peptides. Score 0.249 Round 2: 145 peptides, 26 chains. Longest chain 12 peptides. Score 0.343 Round 3: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.346 Round 4: 168 peptides, 27 chains. Longest chain 12 peptides. Score 0.412 Round 5: 168 peptides, 28 chains. Longest chain 17 peptides. Score 0.397 Taking the results from Round 4 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8875 restraints for refining 3589 atoms. 8338 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1729 (Rfree = 0.000) for 3589 atoms. Found 22 (23 requested) and removed 26 (11 requested) atoms. Cycle 27: After refmac, R = 0.1797 (Rfree = 0.000) for 3579 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 28: After refmac, R = 0.1873 (Rfree = 0.000) for 3580 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 29: After refmac, R = 0.1475 (Rfree = 0.000) for 3565 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 30: After refmac, R = 0.1622 (Rfree = 0.000) for 3566 atoms. Found 18 (22 requested) and removed 58 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3657 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 8 peptides. Score 0.233 Round 2: 172 peptides, 33 chains. Longest chain 12 peptides. Score 0.331 Round 3: 164 peptides, 33 chains. Longest chain 8 peptides. Score 0.300 Round 4: 167 peptides, 32 chains. Longest chain 10 peptides. Score 0.329 Round 5: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.318 Taking the results from Round 2 Chains 33, Residues 139, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8836 restraints for refining 3571 atoms. 8290 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1907 (Rfree = 0.000) for 3571 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 32: After refmac, R = 0.1872 (Rfree = 0.000) for 3562 atoms. Found 22 (22 requested) and removed 63 (11 requested) atoms. Cycle 33: After refmac, R = 0.2005 (Rfree = 0.000) for 3508 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 34: After refmac, R = 0.1751 (Rfree = 0.000) for 3497 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 35: After refmac, R = 0.1707 (Rfree = 0.000) for 3480 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.88 Search for helices and strands provided no result - WARNING Search for helices and strands: 0 residues in 0 chains, 3619 seeds are put forward NCS extension: 0 residues added, 3619 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 7 peptides. Score 0.257 Round 2: 138 peptides, 27 chains. Longest chain 13 peptides. Score 0.298 Round 3: 140 peptides, 26 chains. Longest chain 13 peptides. Score 0.323 Round 4: 146 peptides, 28 chains. Longest chain 9 peptides. Score 0.313 Round 5: 161 peptides, 29 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Chains 29, Residues 132, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8597 restraints for refining 3553 atoms. 8073 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1874 (Rfree = 0.000) for 3553 atoms. Found 22 (22 requested) and removed 71 (11 requested) atoms. Cycle 37: After refmac, R = 0.1755 (Rfree = 0.000) for 3496 atoms. Found 12 (22 requested) and removed 58 (11 requested) atoms. Cycle 38: After refmac, R = 0.1688 (Rfree = 0.000) for 3449 atoms. Found 10 (22 requested) and removed 21 (11 requested) atoms. Cycle 39: After refmac, R = 0.1748 (Rfree = 0.000) for 3435 atoms. Found 20 (22 requested) and removed 16 (11 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 3437 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3577 seeds are put forward Round 1: 113 peptides, 27 chains. Longest chain 6 peptides. Score 0.190 Round 2: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.257 Round 3: 145 peptides, 30 chains. Longest chain 10 peptides. Score 0.275 Round 4: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.347 Round 5: 151 peptides, 28 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 4 Chains 26, Residues 120, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8432 restraints for refining 3510 atoms. 7954 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1919 (Rfree = 0.000) for 3510 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 42: After refmac, R = 0.2213 (Rfree = 0.000) for 3483 atoms. Found 22 (22 requested) and removed 54 (11 requested) atoms. Cycle 43: After refmac, R = 0.1821 (Rfree = 0.000) for 3443 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 44: After refmac, R = 0.1753 (Rfree = 0.000) for 3434 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 3436 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 0 residues added, 3565 seeds are put forward Round 1: 122 peptides, 28 chains. Longest chain 9 peptides. Score 0.212 Round 2: 127 peptides, 27 chains. Longest chain 6 peptides. Score 0.252 Round 3: 147 peptides, 28 chains. Longest chain 11 peptides. Score 0.317 Round 4: 132 peptides, 24 chains. Longest chain 10 peptides. Score 0.326 Round 5: 143 peptides, 27 chains. Longest chain 9 peptides. Score 0.318 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 108, 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. 4971 reflections ( 96.02 % complete ) and 8736 restraints for refining 3529 atoms. 8328 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1952 (Rfree = 0.000) for 3529 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1790 (Rfree = 0.000) for 3517 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1723 (Rfree = 0.000) for 3504 atoms. Found 0 (22 requested) and removed 7 (11 requested) atoms. Cycle 49: After refmac, R = 0.1666 (Rfree = 0.000) for 3497 atoms. Found 0 (22 requested) and removed 2 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:41 GMT 2018 Job finished. TimeTaking 53.65 Used memory is bytes: 14344136