null Mon 24 Dec 07:39:54 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 2it9-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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/2it9-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 07:39:59 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/2it9-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.8-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.800 Wilson plot Bfac: 81.37 6215 reflections ( 98.15 % complete ) and 0 restraints for refining 4537 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3857 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3462 (Rfree = 0.000) for 4537 atoms. Found 24 (24 requested) and removed 54 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 4574 seeds are put forward NCS extension: 0 residues added, 4574 seeds are put forward Round 1: 172 peptides, 37 chains. Longest chain 9 peptides. Score 0.247 Round 2: 217 peptides, 40 chains. Longest chain 13 peptides. Score 0.344 Round 3: 217 peptides, 35 chains. Longest chain 14 peptides. Score 0.405 Round 4: 225 peptides, 40 chains. Longest chain 17 peptides. Score 0.367 Round 5: 244 peptides, 38 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Chains 38, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8479 restraints for refining 3676 atoms. 7693 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2983 (Rfree = 0.000) for 3676 atoms. Found 13 (20 requested) and removed 33 (10 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 3609 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2524 (Rfree = 0.000) for 3594 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 4: After refmac, R = 0.2596 (Rfree = 0.000) for 3565 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 5: After refmac, R = 0.2415 (Rfree = 0.000) for 3555 atoms. Found 16 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3693 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3715 seeds are put forward Round 1: 192 peptides, 37 chains. Longest chain 10 peptides. Score 0.309 Round 2: 227 peptides, 41 chains. Longest chain 10 peptides. Score 0.360 Round 3: 223 peptides, 33 chains. Longest chain 14 peptides. Score 0.444 Round 4: 231 peptides, 35 chains. Longest chain 13 peptides. Score 0.442 Round 5: 222 peptides, 37 chains. Longest chain 25 peptides. Score 0.394 Taking the results from Round 3 Chains 33, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8397 restraints for refining 3614 atoms. 7670 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2608 (Rfree = 0.000) for 3614 atoms. Found 16 (19 requested) and removed 32 (9 requested) atoms. Cycle 7: After refmac, R = 0.2531 (Rfree = 0.000) for 3575 atoms. Found 17 (19 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.2477 (Rfree = 0.000) for 3539 atoms. Found 16 (19 requested) and removed 28 (9 requested) atoms. Cycle 9: After refmac, R = 0.2509 (Rfree = 0.000) for 3505 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 10: After refmac, R = 0.2430 (Rfree = 0.000) for 3493 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 3621 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3636 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 10 peptides. Score 0.303 Round 2: 252 peptides, 45 chains. Longest chain 14 peptides. Score 0.382 Round 3: 240 peptides, 40 chains. Longest chain 18 peptides. Score 0.408 Round 4: 254 peptides, 44 chains. Longest chain 12 peptides. Score 0.399 Round 5: 252 peptides, 41 chains. Longest chain 12 peptides. Score 0.428 Taking the results from Round 5 Chains 41, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8350 restraints for refining 3676 atoms. 7547 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2330 (Rfree = 0.000) for 3676 atoms. Found 10 (20 requested) and removed 26 (10 requested) atoms. Cycle 12: After refmac, R = 0.2133 (Rfree = 0.000) for 3641 atoms. Found 13 (20 requested) and removed 22 (10 requested) atoms. Cycle 13: After refmac, R = 0.2184 (Rfree = 0.000) for 3625 atoms. Found 14 (19 requested) and removed 21 (9 requested) atoms. Cycle 14: After refmac, R = 0.2009 (Rfree = 0.000) for 3611 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2010 (Rfree = 0.000) for 3593 atoms. Found 13 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3724 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3739 seeds are put forward Round 1: 208 peptides, 45 chains. Longest chain 7 peptides. Score 0.256 Round 2: 224 peptides, 39 chains. Longest chain 12 peptides. Score 0.376 Round 3: 234 peptides, 42 chains. Longest chain 12 peptides. Score 0.368 Round 4: 225 peptides, 37 chains. Longest chain 12 peptides. Score 0.403 Round 5: 240 peptides, 39 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 5 Chains 39, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8323 restraints for refining 3676 atoms. 7558 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 3676 atoms. Found 18 (20 requested) and removed 24 (10 requested) atoms. Cycle 17: After refmac, R = 0.2053 (Rfree = 0.000) for 3654 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 18: After refmac, R = 0.2088 (Rfree = 0.000) for 3652 atoms. Found 18 (20 requested) and removed 23 (10 requested) atoms. Cycle 19: After refmac, R = 0.1944 (Rfree = 0.000) for 3639 atoms. Found 19 (20 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.1643 (Rfree = 0.000) for 3638 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3774 seeds are put forward Round 1: 212 peptides, 43 chains. Longest chain 9 peptides. Score 0.293 Round 2: 236 peptides, 41 chains. Longest chain 12 peptides. Score 0.385 Round 3: 239 peptides, 42 chains. Longest chain 11 peptides. Score 0.382 Round 4: 245 peptides, 40 chains. Longest chain 14 peptides. Score 0.421 Round 5: 235 peptides, 37 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 37, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8362 restraints for refining 3676 atoms. 7607 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2306 (Rfree = 0.000) for 3676 atoms. Found 13 (20 requested) and removed 22 (10 requested) atoms. Cycle 22: After refmac, R = 0.2234 (Rfree = 0.000) for 3644 atoms. Found 16 (20 requested) and removed 20 (10 requested) atoms. Cycle 23: After refmac, R = 0.1887 (Rfree = 0.000) for 3633 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1776 (Rfree = 0.000) for 3619 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1735 (Rfree = 0.000) for 3612 atoms. Found 2 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3743 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 12 peptides. Score 0.259 Round 2: 208 peptides, 35 chains. Longest chain 16 peptides. Score 0.380 Round 3: 209 peptides, 36 chains. Longest chain 12 peptides. Score 0.371 Round 4: 209 peptides, 36 chains. Longest chain 10 peptides. Score 0.371 Round 5: 192 peptides, 31 chains. Longest chain 11 peptides. Score 0.385 Taking the results from Round 5 Chains 31, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8684 restraints for refining 3676 atoms. 8071 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2403 (Rfree = 0.000) for 3676 atoms. Found 14 (20 requested) and removed 22 (10 requested) atoms. Cycle 27: After refmac, R = 0.2226 (Rfree = 0.000) for 3656 atoms. Found 17 (20 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.2178 (Rfree = 0.000) for 3649 atoms. Found 18 (20 requested) and removed 18 (10 requested) atoms. Cycle 29: After refmac, R = 0.1815 (Rfree = 0.000) for 3639 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1768 (Rfree = 0.000) for 3628 atoms. Found 0 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3737 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 7 peptides. Score 0.258 Round 2: 233 peptides, 45 chains. Longest chain 9 peptides. Score 0.329 Round 3: 214 peptides, 40 chains. Longest chain 10 peptides. Score 0.336 Round 4: 211 peptides, 37 chains. Longest chain 11 peptides. Score 0.364 Round 5: 209 peptides, 39 chains. Longest chain 9 peptides. Score 0.334 Taking the results from Round 4 Chains 37, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8470 restraints for refining 3676 atoms. 7811 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2198 (Rfree = 0.000) for 3676 atoms. Found 7 (20 requested) and removed 17 (10 requested) atoms. Cycle 32: After refmac, R = 0.2080 (Rfree = 0.000) for 3657 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.2035 (Rfree = 0.000) for 3646 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.1775 (Rfree = 0.000) for 3636 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 3625 atoms. Found 0 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 3706 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3720 seeds are put forward Round 1: 166 peptides, 34 chains. Longest chain 8 peptides. Score 0.268 Round 2: 184 peptides, 34 chains. Longest chain 11 peptides. Score 0.323 Round 3: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.344 Round 4: 197 peptides, 35 chains. Longest chain 13 peptides. Score 0.349 Round 5: 192 peptides, 32 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 5 Chains 32, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8484 restraints for refining 3676 atoms. 7876 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2182 (Rfree = 0.000) for 3676 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.2175 (Rfree = 0.000) for 3665 atoms. Found 17 (20 requested) and removed 21 (10 requested) atoms. Cycle 38: After refmac, R = 0.1757 (Rfree = 0.000) for 3657 atoms. Found 2 (20 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1702 (Rfree = 0.000) for 3643 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 40: After refmac, R = 0.1675 (Rfree = 0.000) for 3632 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3722 seeds are put forward Round 1: 164 peptides, 36 chains. Longest chain 7 peptides. Score 0.235 Round 2: 173 peptides, 33 chains. Longest chain 12 peptides. Score 0.303 Round 3: 172 peptides, 32 chains. Longest chain 12 peptides. Score 0.313 Round 4: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.326 Round 5: 180 peptides, 34 chains. Longest chain 12 peptides. Score 0.311 Taking the results from Round 4 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8494 restraints for refining 3676 atoms. 7987 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 42: After refmac, R = 0.2049 (Rfree = 0.000) for 3668 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 43: After refmac, R = 0.2013 (Rfree = 0.000) for 3665 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.2008 (Rfree = 0.000) for 3667 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.1600 (Rfree = 0.000) for 3672 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3763 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3766 seeds are put forward Round 1: 157 peptides, 33 chains. Longest chain 9 peptides. Score 0.253 Round 2: 176 peptides, 35 chains. Longest chain 9 peptides. Score 0.286 Round 3: 191 peptides, 37 chains. Longest chain 9 peptides. Score 0.306 Round 4: 177 peptides, 33 chains. Longest chain 9 peptides. Score 0.315 Round 5: 174 peptides, 32 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 142, 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 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6215 reflections ( 98.15 % complete ) and 8481 restraints for refining 3676 atoms. 7945 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2105 (Rfree = 0.000) for 3676 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2189 (Rfree = 0.000) for 3654 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2037 (Rfree = 0.000) for 3635 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1726 (Rfree = 0.000) for 3621 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:21:01 GMT 2018 Job finished. TimeTaking 41.11 Used memory is bytes: 154968