Mon 24 Dec 00:59:51 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 2it9-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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/2it9-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 00:59:55 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/2it9-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 393 and 0 Target number of residues in the AU: 393 Target solvent content: 0.6465 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: 2it9-3.6-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 75.92 7278 reflections ( 98.28 % complete ) and 0 restraints for refining 4500 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3561 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3177 (Rfree = 0.000) for 4500 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 4591 seeds are put forward NCS extension: 0 residues added, 4591 seeds are put forward Round 1: 243 peptides, 42 chains. Longest chain 16 peptides. Score 0.393 Round 2: 287 peptides, 43 chains. Longest chain 16 peptides. Score 0.493 Round 3: 296 peptides, 39 chains. Longest chain 17 peptides. Score 0.554 Round 4: 308 peptides, 41 chains. Longest chain 17 peptides. Score 0.560 Round 5: 328 peptides, 40 chains. Longest chain 19 peptides. Score 0.610 Taking the results from Round 5 Chains 40, Residues 288, Estimated correctness of the model 18.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8064 restraints for refining 3684 atoms. 6952 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2523 (Rfree = 0.000) for 3684 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 2: After refmac, R = 0.2278 (Rfree = 0.000) for 3648 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 3: After refmac, R = 0.2210 (Rfree = 0.000) for 3630 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2222 (Rfree = 0.000) for 3619 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2216 (Rfree = 0.000) for 3609 atoms. Found 8 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3761 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3783 seeds are put forward Round 1: 265 peptides, 45 chains. Longest chain 13 peptides. Score 0.417 Round 2: 299 peptides, 41 chains. Longest chain 17 peptides. Score 0.541 Round 3: 304 peptides, 37 chains. Longest chain 25 peptides. Score 0.589 Round 4: 300 peptides, 37 chains. Longest chain 20 peptides. Score 0.581 Round 5: 303 peptides, 41 chains. Longest chain 15 peptides. Score 0.549 Taking the results from Round 3 Chains 38, Residues 267, Estimated correctness of the model 10.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7278 reflections ( 98.28 % complete ) and 8019 restraints for refining 3684 atoms. 6950 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 3684 atoms. Found 21 (23 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.2153 (Rfree = 0.000) for 3662 atoms. Found 21 (23 requested) and removed 18 (11 requested) atoms. Cycle 8: After refmac, R = 0.2021 (Rfree = 0.000) for 3658 atoms. Found 14 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.1968 (Rfree = 0.000) for 3652 atoms. Found 4 (23 requested) and removed 17 (11 requested) atoms. Cycle 10: After refmac, R = 0.1973 (Rfree = 0.000) for 3634 atoms. Found 7 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3810 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 3842 seeds are put forward Round 1: 280 peptides, 43 chains. Longest chain 14 peptides. Score 0.476 Round 2: 317 peptides, 43 chains. Longest chain 20 peptides. Score 0.560 Round 3: 306 peptides, 43 chains. Longest chain 17 peptides. Score 0.536 Round 4: 323 peptides, 40 chains. Longest chain 19 peptides. Score 0.600 Round 5: 316 peptides, 41 chains. Longest chain 16 peptides. Score 0.577 Taking the results from Round 4 Chains 42, Residues 283, Estimated correctness of the model 14.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8015 restraints for refining 3684 atoms. 6874 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2240 (Rfree = 0.000) for 3684 atoms. Found 22 (23 requested) and removed 22 (11 requested) atoms. Cycle 12: After refmac, R = 0.2102 (Rfree = 0.000) for 3663 atoms. Found 17 (23 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.1959 (Rfree = 0.000) for 3663 atoms. Found 14 (23 requested) and removed 18 (11 requested) atoms. Cycle 14: After refmac, R = 0.1964 (Rfree = 0.000) for 3657 atoms. Found 14 (23 requested) and removed 18 (11 requested) atoms. Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 3649 atoms. Found 10 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3797 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3815 seeds are put forward Round 1: 266 peptides, 44 chains. Longest chain 15 peptides. Score 0.430 Round 2: 292 peptides, 41 chains. Longest chain 20 peptides. Score 0.525 Round 3: 287 peptides, 40 chains. Longest chain 17 peptides. Score 0.524 Round 4: 292 peptides, 42 chains. Longest chain 20 peptides. Score 0.515 Round 5: 307 peptides, 41 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 5 Chains 41, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8268 restraints for refining 3684 atoms. 7245 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 3684 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.2192 (Rfree = 0.000) for 3663 atoms. Found 15 (23 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.2082 (Rfree = 0.000) for 3649 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 3628 atoms. Found 15 (23 requested) and removed 18 (11 requested) atoms. Cycle 20: After refmac, R = 0.1987 (Rfree = 0.000) for 3620 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3763 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3779 seeds are put forward Round 1: 248 peptides, 45 chains. Longest chain 15 peptides. Score 0.371 Round 2: 292 peptides, 45 chains. Longest chain 15 peptides. Score 0.484 Round 3: 274 peptides, 40 chains. Longest chain 25 peptides. Score 0.493 Round 4: 275 peptides, 40 chains. Longest chain 22 peptides. Score 0.496 Round 5: 258 peptides, 36 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 5 Chains 36, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8423 restraints for refining 3684 atoms. 7571 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2222 (Rfree = 0.000) for 3684 atoms. Found 22 (23 requested) and removed 17 (11 requested) atoms. Cycle 22: After refmac, R = 0.1950 (Rfree = 0.000) for 3678 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1852 (Rfree = 0.000) for 3668 atoms. Found 7 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1805 (Rfree = 0.000) for 3659 atoms. Found 3 (23 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.1771 (Rfree = 0.000) for 3641 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3740 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 3760 seeds are put forward Round 1: 252 peptides, 49 chains. Longest chain 10 peptides. Score 0.335 Round 2: 275 peptides, 42 chains. Longest chain 17 peptides. Score 0.475 Round 3: 271 peptides, 39 chains. Longest chain 17 peptides. Score 0.497 Round 4: 282 peptides, 39 chains. Longest chain 13 peptides. Score 0.522 Round 5: 284 peptides, 40 chains. Longest chain 12 peptides. Score 0.517 Taking the results from Round 4 Chains 39, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8274 restraints for refining 3683 atoms. 7341 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 3683 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 27: After refmac, R = 0.1951 (Rfree = 0.000) for 3672 atoms. Found 10 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1903 (Rfree = 0.000) for 3664 atoms. Found 7 (23 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 3654 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1866 (Rfree = 0.000) for 3645 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3758 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3772 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 11 peptides. Score 0.353 Round 2: 244 peptides, 37 chains. Longest chain 19 peptides. Score 0.452 Round 3: 254 peptides, 41 chains. Longest chain 12 peptides. Score 0.433 Round 4: 267 peptides, 41 chains. Longest chain 15 peptides. Score 0.466 Round 5: 266 peptides, 38 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 5 Chains 38, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8396 restraints for refining 3684 atoms. 7522 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 3684 atoms. Found 15 (23 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.2011 (Rfree = 0.000) for 3668 atoms. Found 8 (23 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.1975 (Rfree = 0.000) for 3656 atoms. Found 5 (23 requested) and removed 15 (11 requested) atoms. Cycle 34: After refmac, R = 0.1938 (Rfree = 0.000) for 3644 atoms. Found 10 (23 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1894 (Rfree = 0.000) for 3640 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3770 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3783 seeds are put forward Round 1: 216 peptides, 41 chains. Longest chain 11 peptides. Score 0.329 Round 2: 241 peptides, 36 chains. Longest chain 13 peptides. Score 0.456 Round 3: 250 peptides, 37 chains. Longest chain 12 peptides. Score 0.467 Round 4: 252 peptides, 37 chains. Longest chain 16 peptides. Score 0.472 Round 5: 252 peptides, 39 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 4 Chains 37, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8494 restraints for refining 3684 atoms. 7671 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2182 (Rfree = 0.000) for 3684 atoms. Found 20 (23 requested) and removed 13 (11 requested) atoms. Cycle 37: After refmac, R = 0.2087 (Rfree = 0.000) for 3683 atoms. Found 12 (23 requested) and removed 14 (11 requested) atoms. Cycle 38: After refmac, R = 0.1941 (Rfree = 0.000) for 3679 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1926 (Rfree = 0.000) for 3668 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1836 (Rfree = 0.000) for 3662 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 3749 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3778 seeds are put forward Round 1: 208 peptides, 39 chains. Longest chain 12 peptides. Score 0.331 Round 2: 234 peptides, 38 chains. Longest chain 13 peptides. Score 0.415 Round 3: 226 peptides, 38 chains. Longest chain 13 peptides. Score 0.393 Round 4: 217 peptides, 38 chains. Longest chain 12 peptides. Score 0.369 Round 5: 233 peptides, 37 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Chains 38, Residues 196, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8412 restraints for refining 3684 atoms. 7623 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2176 (Rfree = 0.000) for 3684 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. Cycle 42: After refmac, R = 0.1974 (Rfree = 0.000) for 3677 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.1898 (Rfree = 0.000) for 3665 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1859 (Rfree = 0.000) for 3653 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1856 (Rfree = 0.000) for 3642 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 3742 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3755 seeds are put forward Round 1: 198 peptides, 37 chains. Longest chain 10 peptides. Score 0.327 Round 2: 240 peptides, 38 chains. Longest chain 13 peptides. Score 0.431 Round 3: 243 peptides, 38 chains. Longest chain 13 peptides. Score 0.438 Round 4: 236 peptides, 35 chains. Longest chain 16 peptides. Score 0.454 Round 5: 238 peptides, 36 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 201, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7278 reflections ( 98.28 % complete ) and 8443 restraints for refining 3684 atoms. 7644 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2135 (Rfree = 0.000) for 3684 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1941 (Rfree = 0.000) for 3662 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1915 (Rfree = 0.000) for 3644 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1864 (Rfree = 0.000) for 3631 atoms. Found 0 (23 requested) and removed 2 (11 requested) atoms. Writing output files ... TimeTaking 40.92