null Mon 24 Dec 07:46:42 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 2p7i-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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/2p7i-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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 07:46:46 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/2p7i-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6574 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.6-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.600 Wilson plot Bfac: 83.07 6704 reflections ( 99.70 % complete ) and 0 restraints for refining 4442 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3271 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3109 (Rfree = 0.000) for 4442 atoms. Found 17 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 4519 seeds are put forward NCS extension: 0 residues added, 4519 seeds are put forward Round 1: 212 peptides, 47 chains. Longest chain 8 peptides. Score 0.248 Round 2: 285 peptides, 42 chains. Longest chain 18 peptides. Score 0.522 Round 3: 288 peptides, 38 chains. Longest chain 18 peptides. Score 0.572 Round 4: 291 peptides, 37 chains. Longest chain 19 peptides. Score 0.589 Round 5: 299 peptides, 36 chains. Longest chain 19 peptides. Score 0.616 Taking the results from Round 5 Chains 38, Residues 263, Estimated correctness of the model 20.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8041 restraints for refining 3625 atoms. 6991 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2613 (Rfree = 0.000) for 3625 atoms. Found 16 (23 requested) and removed 25 (11 requested) atoms. Cycle 2: After refmac, R = 0.2536 (Rfree = 0.000) for 3549 atoms. Found 15 (23 requested) and removed 14 (11 requested) atoms. Cycle 3: After refmac, R = 0.2412 (Rfree = 0.000) for 3523 atoms. Found 8 (22 requested) and removed 16 (11 requested) atoms. Cycle 4: After refmac, R = 0.2262 (Rfree = 0.000) for 3494 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2257 (Rfree = 0.000) for 3481 atoms. Found 10 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 3634 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3647 seeds are put forward Round 1: 246 peptides, 42 chains. Longest chain 16 peptides. Score 0.418 Round 2: 279 peptides, 38 chains. Longest chain 15 peptides. Score 0.551 Round 3: 287 peptides, 37 chains. Longest chain 17 peptides. Score 0.580 Round 4: 302 peptides, 40 chains. Longest chain 16 peptides. Score 0.583 Round 5: 293 peptides, 35 chains. Longest chain 17 peptides. Score 0.613 Taking the results from Round 5 Chains 37, Residues 258, Estimated correctness of the model 19.7 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7825 restraints for refining 3626 atoms. 6749 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2409 (Rfree = 0.000) for 3626 atoms. Found 3 (23 requested) and removed 23 (11 requested) atoms. Cycle 7: After refmac, R = 0.2255 (Rfree = 0.000) for 3573 atoms. Found 7 (23 requested) and removed 20 (11 requested) atoms. Cycle 8: After refmac, R = 0.2125 (Rfree = 0.000) for 3544 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.2005 (Rfree = 0.000) for 3527 atoms. Found 3 (22 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2036 (Rfree = 0.000) for 3506 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3617 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3633 seeds are put forward Round 1: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.420 Round 2: 262 peptides, 38 chains. Longest chain 15 peptides. Score 0.509 Round 3: 278 peptides, 38 chains. Longest chain 17 peptides. Score 0.548 Round 4: 259 peptides, 37 chains. Longest chain 22 peptides. Score 0.512 Round 5: 255 peptides, 36 chains. Longest chain 18 peptides. Score 0.513 Taking the results from Round 3 Chains 40, Residues 240, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8137 restraints for refining 3626 atoms. 7183 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2371 (Rfree = 0.000) for 3626 atoms. Found 14 (23 requested) and removed 19 (11 requested) atoms. Cycle 12: After refmac, R = 0.2273 (Rfree = 0.000) for 3603 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 13: After refmac, R = 0.1958 (Rfree = 0.000) for 3576 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2040 (Rfree = 0.000) for 3558 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.1893 (Rfree = 0.000) for 3553 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3664 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3683 seeds are put forward Round 1: 250 peptides, 43 chains. Longest chain 17 peptides. Score 0.417 Round 2: 268 peptides, 36 chains. Longest chain 24 peptides. Score 0.546 Round 3: 269 peptides, 40 chains. Longest chain 16 peptides. Score 0.504 Round 4: 278 peptides, 40 chains. Longest chain 19 peptides. Score 0.527 Round 5: 268 peptides, 36 chains. Longest chain 23 peptides. Score 0.546 Taking the results from Round 5 Chains 36, Residues 232, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7858 restraints for refining 3625 atoms. 6774 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2430 (Rfree = 0.000) for 3625 atoms. Found 22 (23 requested) and removed 22 (11 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 3586 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.1927 (Rfree = 0.000) for 3568 atoms. Found 5 (22 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.1959 (Rfree = 0.000) for 3553 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1787 (Rfree = 0.000) for 3541 atoms. Found 6 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 3633 seeds are put forward NCS extension: 41 residues added (0 deleted due to clashes), 3674 seeds are put forward Round 1: 211 peptides, 36 chains. Longest chain 13 peptides. Score 0.391 Round 2: 243 peptides, 38 chains. Longest chain 16 peptides. Score 0.458 Round 3: 254 peptides, 34 chains. Longest chain 23 peptides. Score 0.533 Round 4: 269 peptides, 34 chains. Longest chain 25 peptides. Score 0.569 Round 5: 272 peptides, 38 chains. Longest chain 15 peptides. Score 0.534 Taking the results from Round 4 Chains 35, Residues 235, Estimated correctness of the model 2.2 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8207 restraints for refining 3626 atoms. 7270 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2226 (Rfree = 0.000) for 3626 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. Cycle 22: After refmac, R = 0.1971 (Rfree = 0.000) for 3614 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 3604 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.1928 (Rfree = 0.000) for 3588 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.1922 (Rfree = 0.000) for 3576 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 3703 seeds are put forward Round 1: 200 peptides, 38 chains. Longest chain 10 peptides. Score 0.331 Round 2: 244 peptides, 42 chains. Longest chain 13 peptides. Score 0.412 Round 3: 238 peptides, 36 chains. Longest chain 15 peptides. Score 0.469 Round 4: 251 peptides, 39 chains. Longest chain 15 peptides. Score 0.468 Round 5: 258 peptides, 36 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 37, Residues 222, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8358 restraints for refining 3626 atoms. 7463 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2096 (Rfree = 0.000) for 3626 atoms. Found 8 (23 requested) and removed 34 (11 requested) atoms. Cycle 27: After refmac, R = 0.2004 (Rfree = 0.000) for 3588 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 28: After refmac, R = 0.2037 (Rfree = 0.000) for 3578 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.2050 (Rfree = 0.000) for 3575 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1991 (Rfree = 0.000) for 3570 atoms. Found 15 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 3684 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3714 seeds are put forward Round 1: 192 peptides, 37 chains. Longest chain 13 peptides. Score 0.319 Round 2: 210 peptides, 36 chains. Longest chain 15 peptides. Score 0.388 Round 3: 223 peptides, 33 chains. Longest chain 15 peptides. Score 0.464 Round 4: 231 peptides, 37 chains. Longest chain 17 peptides. Score 0.437 Round 5: 234 peptides, 34 chains. Longest chain 19 peptides. Score 0.482 Taking the results from Round 5 Chains 35, Residues 200, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8434 restraints for refining 3624 atoms. 7614 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2120 (Rfree = 0.000) for 3624 atoms. Found 16 (23 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.2073 (Rfree = 0.000) for 3614 atoms. Found 17 (23 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.2110 (Rfree = 0.000) for 3604 atoms. Found 20 (23 requested) and removed 16 (11 requested) atoms. Cycle 34: After refmac, R = 0.1918 (Rfree = 0.000) for 3589 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.2021 (Rfree = 0.000) for 3582 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3674 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3695 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 18 peptides. Score 0.313 Round 2: 209 peptides, 32 chains. Longest chain 18 peptides. Score 0.437 Round 3: 217 peptides, 36 chains. Longest chain 17 peptides. Score 0.409 Round 4: 205 peptides, 32 chains. Longest chain 18 peptides. Score 0.425 Round 5: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8608 restraints for refining 3626 atoms. 7935 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2393 (Rfree = 0.000) for 3626 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.2064 (Rfree = 0.000) for 3613 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.1972 (Rfree = 0.000) for 3608 atoms. Found 21 (23 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.1557 (Rfree = 0.000) for 3604 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1483 (Rfree = 0.000) for 3592 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3701 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3718 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.264 Round 2: 179 peptides, 30 chains. Longest chain 15 peptides. Score 0.374 Round 3: 176 peptides, 28 chains. Longest chain 15 peptides. Score 0.392 Round 4: 172 peptides, 27 chains. Longest chain 18 peptides. Score 0.393 Round 5: 175 peptides, 28 chains. Longest chain 12 peptides. Score 0.389 Taking the results from Round 4 Chains 27, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8568 restraints for refining 3589 atoms. 8015 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2143 (Rfree = 0.000) for 3589 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 42: After refmac, R = 0.1868 (Rfree = 0.000) for 3579 atoms. Found 16 (23 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.2034 (Rfree = 0.000) for 3575 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.1754 (Rfree = 0.000) for 3575 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.1939 (Rfree = 0.000) for 3563 atoms. Found 20 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.50 Search for helices and strands: 0 residues in 0 chains, 3676 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3702 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 8 peptides. Score 0.266 Round 2: 189 peptides, 35 chains. Longest chain 13 peptides. Score 0.337 Round 3: 186 peptides, 32 chains. Longest chain 13 peptides. Score 0.368 Round 4: 190 peptides, 34 chains. Longest chain 11 peptides. Score 0.354 Round 5: 185 peptides, 32 chains. Longest chain 10 peptides. Score 0.365 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 154, 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 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6704 reflections ( 99.70 % complete ) and 8534 restraints for refining 3607 atoms. 7950 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1902 (Rfree = 0.000) for 3607 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2011 (Rfree = 0.000) for 3583 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 3568 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2001 (Rfree = 0.000) for 3547 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:31:19 GMT 2018 Job finished. TimeTaking 44.63 Used memory is bytes: -124216