null Mon 24 Dec 00:51:43 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 2i5i-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-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/2i5i-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-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 ============================================================ Mon 24 Dec 00:51:48 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/2i5i-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.6-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-3.6-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 3.600 Wilson plot Bfac: 78.40 6266 reflections ( 99.19 % complete ) and 0 restraints for refining 4647 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3380 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3075 (Rfree = 0.000) for 4647 atoms. Found 29 (29 requested) and removed 75 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 4646 seeds are put forward NCS extension: 0 residues added, 4646 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 7 peptides. Score 0.221 Round 2: 178 peptides, 37 chains. Longest chain 8 peptides. Score 0.271 Round 3: 220 peptides, 42 chains. Longest chain 11 peptides. Score 0.337 Round 4: 227 peptides, 41 chains. Longest chain 10 peptides. Score 0.371 Round 5: 242 peptides, 45 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 4 Chains 41, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8966 restraints for refining 3815 atoms. 8263 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2288 (Rfree = 0.000) for 3815 atoms. Found 18 (24 requested) and removed 25 (12 requested) atoms. Cycle 2: After refmac, R = 0.2230 (Rfree = 0.000) for 3744 atoms. Found 11 (24 requested) and removed 15 (12 requested) atoms. Cycle 3: After refmac, R = 0.2322 (Rfree = 0.000) for 3706 atoms. Found 14 (23 requested) and removed 21 (11 requested) atoms. Cycle 4: After refmac, R = 0.2189 (Rfree = 0.000) for 3678 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2178 (Rfree = 0.000) for 3656 atoms. Found 8 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3739 seeds are put forward Round 1: 187 peptides, 42 chains. Longest chain 7 peptides. Score 0.232 Round 2: 231 peptides, 47 chains. Longest chain 11 peptides. Score 0.306 Round 3: 236 peptides, 46 chains. Longest chain 10 peptides. Score 0.334 Round 4: 227 peptides, 43 chains. Longest chain 10 peptides. Score 0.345 Round 5: 239 peptides, 45 chains. Longest chain 14 peptides. Score 0.356 Taking the results from Round 5 Chains 45, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8226 restraints for refining 3591 atoms. 7495 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2072 (Rfree = 0.000) for 3591 atoms. Found 16 (23 requested) and removed 27 (11 requested) atoms. Cycle 7: After refmac, R = 0.1933 (Rfree = 0.000) for 3554 atoms. Found 8 (22 requested) and removed 18 (11 requested) atoms. Cycle 8: After refmac, R = 0.1842 (Rfree = 0.000) for 3533 atoms. Found 8 (22 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.1786 (Rfree = 0.000) for 3521 atoms. Found 7 (22 requested) and removed 18 (11 requested) atoms. Cycle 10: After refmac, R = 0.1780 (Rfree = 0.000) for 3502 atoms. Found 10 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3612 seeds are put forward NCS extension: 0 residues added, 3612 seeds are put forward Round 1: 219 peptides, 48 chains. Longest chain 9 peptides. Score 0.256 Round 2: 233 peptides, 42 chains. Longest chain 11 peptides. Score 0.376 Round 3: 251 peptides, 45 chains. Longest chain 11 peptides. Score 0.390 Round 4: 242 peptides, 41 chains. Longest chain 12 peptides. Score 0.414 Round 5: 232 peptides, 40 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 4 Chains 41, Residues 201, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8451 restraints for refining 3739 atoms. 7643 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2130 (Rfree = 0.000) for 3739 atoms. Found 20 (24 requested) and removed 38 (12 requested) atoms. Cycle 12: After refmac, R = 0.2099 (Rfree = 0.000) for 3693 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 13: After refmac, R = 0.1837 (Rfree = 0.000) for 3667 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Cycle 14: After refmac, R = 0.1797 (Rfree = 0.000) for 3652 atoms. Found 13 (23 requested) and removed 20 (11 requested) atoms. Cycle 15: After refmac, R = 0.1761 (Rfree = 0.000) for 3633 atoms. Found 10 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 3698 seeds are put forward NCS extension: 0 residues added, 3698 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 10 peptides. Score 0.284 Round 2: 237 peptides, 43 chains. Longest chain 11 peptides. Score 0.375 Round 3: 237 peptides, 41 chains. Longest chain 13 peptides. Score 0.399 Round 4: 221 peptides, 41 chains. Longest chain 11 peptides. Score 0.353 Round 5: 225 peptides, 38 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 5 Chains 39, Residues 187, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8365 restraints for refining 3742 atoms. 7616 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1799 (Rfree = 0.000) for 3742 atoms. Found 22 (24 requested) and removed 31 (12 requested) atoms. Cycle 17: After refmac, R = 0.1708 (Rfree = 0.000) for 3713 atoms. Found 18 (23 requested) and removed 19 (11 requested) atoms. Cycle 18: After refmac, R = 0.1687 (Rfree = 0.000) for 3703 atoms. Found 17 (23 requested) and removed 20 (11 requested) atoms. Cycle 19: After refmac, R = 0.1613 (Rfree = 0.000) for 3699 atoms. Found 15 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1650 (Rfree = 0.000) for 3694 atoms. Found 15 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 3748 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3767 seeds are put forward Round 1: 204 peptides, 44 chains. Longest chain 14 peptides. Score 0.261 Round 2: 233 peptides, 42 chains. Longest chain 15 peptides. Score 0.376 Round 3: 227 peptides, 40 chains. Longest chain 15 peptides. Score 0.383 Round 4: 229 peptides, 39 chains. Longest chain 16 peptides. Score 0.401 Round 5: 241 peptides, 41 chains. Longest chain 16 peptides. Score 0.411 Taking the results from Round 5 Chains 42, Residues 200, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8521 restraints for refining 3815 atoms. 7710 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1763 (Rfree = 0.000) for 3815 atoms. Found 17 (24 requested) and removed 23 (12 requested) atoms. Cycle 22: After refmac, R = 0.1685 (Rfree = 0.000) for 3791 atoms. Found 14 (24 requested) and removed 19 (12 requested) atoms. Cycle 23: After refmac, R = 0.1581 (Rfree = 0.000) for 3779 atoms. Found 10 (24 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1622 (Rfree = 0.000) for 3768 atoms. Found 20 (24 requested) and removed 20 (12 requested) atoms. Cycle 25: After refmac, R = 0.1575 (Rfree = 0.000) for 3763 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 3851 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3869 seeds are put forward Round 1: 196 peptides, 42 chains. Longest chain 9 peptides. Score 0.262 Round 2: 223 peptides, 41 chains. Longest chain 12 peptides. Score 0.359 Round 3: 217 peptides, 38 chains. Longest chain 11 peptides. Score 0.379 Round 4: 208 peptides, 35 chains. Longest chain 18 peptides. Score 0.391 Round 5: 217 peptides, 37 chains. Longest chain 18 peptides. Score 0.392 Taking the results from Round 5 Chains 37, Residues 180, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8707 restraints for refining 3815 atoms. 8013 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1626 (Rfree = 0.000) for 3815 atoms. Found 18 (24 requested) and removed 22 (12 requested) atoms. Cycle 27: After refmac, R = 0.1567 (Rfree = 0.000) for 3803 atoms. Found 17 (24 requested) and removed 20 (12 requested) atoms. Cycle 28: After refmac, R = 0.1571 (Rfree = 0.000) for 3792 atoms. Found 13 (24 requested) and removed 16 (12 requested) atoms. Cycle 29: After refmac, R = 0.1571 (Rfree = 0.000) for 3784 atoms. Found 17 (24 requested) and removed 17 (12 requested) atoms. Cycle 30: After refmac, R = 0.1483 (Rfree = 0.000) for 3782 atoms. Found 11 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3889 seeds are put forward Round 1: 200 peptides, 40 chains. Longest chain 10 peptides. Score 0.301 Round 2: 226 peptides, 43 chains. Longest chain 11 peptides. Score 0.342 Round 3: 222 peptides, 42 chains. Longest chain 13 peptides. Score 0.343 Round 4: 219 peptides, 38 chains. Longest chain 15 peptides. Score 0.385 Round 5: 208 peptides, 35 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 5 Chains 35, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8837 restraints for refining 3815 atoms. 8180 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1651 (Rfree = 0.000) for 3815 atoms. Found 20 (24 requested) and removed 19 (12 requested) atoms. Cycle 32: After refmac, R = 0.1551 (Rfree = 0.000) for 3812 atoms. Found 21 (24 requested) and removed 20 (12 requested) atoms. Cycle 33: After refmac, R = 0.1534 (Rfree = 0.000) for 3810 atoms. Found 20 (24 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.1506 (Rfree = 0.000) for 3811 atoms. Found 16 (24 requested) and removed 18 (12 requested) atoms. Cycle 35: After refmac, R = 0.1403 (Rfree = 0.000) for 3800 atoms. Found 15 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3903 seeds are put forward Round 1: 173 peptides, 38 chains. Longest chain 8 peptides. Score 0.240 Round 2: 197 peptides, 38 chains. Longest chain 10 peptides. Score 0.318 Round 3: 203 peptides, 40 chains. Longest chain 14 peptides. Score 0.311 Round 4: 199 peptides, 37 chains. Longest chain 12 peptides. Score 0.338 Round 5: 200 peptides, 37 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 5 Chains 37, Residues 163, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8750 restraints for refining 3815 atoms. 8093 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1760 (Rfree = 0.000) for 3815 atoms. Found 14 (24 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.1515 (Rfree = 0.000) for 3788 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 38: After refmac, R = 0.1448 (Rfree = 0.000) for 3784 atoms. Found 12 (24 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1372 (Rfree = 0.000) for 3777 atoms. Found 14 (24 requested) and removed 16 (12 requested) atoms. Cycle 40: After refmac, R = 0.1331 (Rfree = 0.000) for 3766 atoms. Found 13 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 3831 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3848 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 7 peptides. Score 0.251 Round 2: 195 peptides, 35 chains. Longest chain 19 peptides. Score 0.352 Round 3: 200 peptides, 36 chains. Longest chain 11 peptides. Score 0.354 Round 4: 202 peptides, 34 chains. Longest chain 14 peptides. Score 0.386 Round 5: 195 peptides, 34 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 4 Chains 34, Residues 168, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8586 restraints for refining 3813 atoms. 7885 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1498 (Rfree = 0.000) for 3813 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.1367 (Rfree = 0.000) for 3815 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.1375 (Rfree = 0.000) for 3808 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.1340 (Rfree = 0.000) for 3799 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.1300 (Rfree = 0.000) for 3792 atoms. Found 2 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3825 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3843 seeds are put forward Round 1: 173 peptides, 38 chains. Longest chain 7 peptides. Score 0.240 Round 2: 199 peptides, 39 chains. Longest chain 12 peptides. Score 0.311 Round 3: 208 peptides, 40 chains. Longest chain 16 peptides. Score 0.326 Round 4: 207 peptides, 36 chains. Longest chain 14 peptides. Score 0.375 Round 5: 215 peptides, 40 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 171, 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 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6266 reflections ( 99.19 % complete ) and 8910 restraints for refining 3813 atoms. 8262 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1490 (Rfree = 0.000) for 3813 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1410 (Rfree = 0.000) for 3790 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1390 (Rfree = 0.000) for 3773 atoms. Found 0 (24 requested) and removed 2 (12 requested) atoms. Cycle 49: After refmac, R = 0.1373 (Rfree = 0.000) for 3769 atoms. Found 0 (24 requested) and removed 1 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:37:04 GMT 2018 Job finished. TimeTaking 45.35 Used memory is bytes: 7956816