Mon 24 Dec 07:55:10 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 2i5i-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-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/2i5i-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-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 07:55:15 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/2i5i-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-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 371 and 0 Target number of residues in the AU: 371 Target solvent content: 0.6430 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-3.4-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.4-parrot-noncs.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 3.401 Wilson plot Bfac: 73.53 7444 reflections ( 99.32 % complete ) and 0 restraints for refining 4665 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3483 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3263 (Rfree = 0.000) for 4665 atoms. Found 35 (35 requested) and removed 85 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 4655 seeds are put forward NCS extension: 0 residues added, 4655 seeds are put forward Round 1: 107 peptides, 25 chains. Longest chain 8 peptides. Score 0.195 Round 2: 138 peptides, 29 chains. Longest chain 11 peptides. Score 0.249 Round 3: 144 peptides, 30 chains. Longest chain 11 peptides. Score 0.255 Round 4: 181 peptides, 35 chains. Longest chain 11 peptides. Score 0.308 Round 5: 194 peptides, 38 chains. Longest chain 12 peptides. Score 0.309 Taking the results from Round 5 Chains 38, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 9036 restraints for refining 3825 atoms. 8450 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2771 (Rfree = 0.000) for 3825 atoms. Found 17 (28 requested) and removed 31 (14 requested) atoms. Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 3761 atoms. Found 18 (28 requested) and removed 24 (14 requested) atoms. Cycle 3: After refmac, R = 0.2659 (Rfree = 0.000) for 3724 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 4: After refmac, R = 0.2584 (Rfree = 0.000) for 3707 atoms. Found 27 (28 requested) and removed 23 (14 requested) atoms. Cycle 5: After refmac, R = 0.2474 (Rfree = 0.000) for 3705 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3774 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3794 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 6 peptides. Score 0.234 Round 2: 208 peptides, 40 chains. Longest chain 9 peptides. Score 0.326 Round 3: 200 peptides, 40 chains. Longest chain 9 peptides. Score 0.301 Round 4: 215 peptides, 42 chains. Longest chain 10 peptides. Score 0.322 Round 5: 205 peptides, 38 chains. Longest chain 12 peptides. Score 0.343 Taking the results from Round 5 Chains 38, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8225 restraints for refining 3593 atoms. 7595 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2404 (Rfree = 0.000) for 3593 atoms. Found 23 (27 requested) and removed 26 (13 requested) atoms. Cycle 7: After refmac, R = 0.2217 (Rfree = 0.000) for 3569 atoms. Found 23 (27 requested) and removed 22 (13 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 3557 atoms. Found 7 (26 requested) and removed 23 (13 requested) atoms. Cycle 9: After refmac, R = 0.2217 (Rfree = 0.000) for 3534 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.1837 (Rfree = 0.000) for 3537 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 3612 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3630 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 11 peptides. Score 0.278 Round 2: 226 peptides, 43 chains. Longest chain 12 peptides. Score 0.342 Round 3: 222 peptides, 41 chains. Longest chain 12 peptides. Score 0.356 Round 4: 215 peptides, 38 chains. Longest chain 14 peptides. Score 0.373 Round 5: 218 peptides, 38 chains. Longest chain 17 peptides. Score 0.382 Taking the results from Round 5 Chains 39, Residues 180, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8019 restraints for refining 3669 atoms. 7238 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2095 (Rfree = 0.000) for 3669 atoms. Found 17 (27 requested) and removed 30 (13 requested) atoms. Cycle 12: After refmac, R = 0.2082 (Rfree = 0.000) for 3631 atoms. Found 23 (27 requested) and removed 22 (13 requested) atoms. Cycle 13: After refmac, R = 0.1975 (Rfree = 0.000) for 3622 atoms. Found 11 (27 requested) and removed 21 (13 requested) atoms. Cycle 14: After refmac, R = 0.2002 (Rfree = 0.000) for 3604 atoms. Found 12 (27 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.1941 (Rfree = 0.000) for 3584 atoms. Found 11 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3652 seeds are put forward Round 1: 198 peptides, 42 chains. Longest chain 10 peptides. Score 0.268 Round 2: 240 peptides, 42 chains. Longest chain 13 peptides. Score 0.396 Round 3: 243 peptides, 42 chains. Longest chain 11 peptides. Score 0.404 Round 4: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.414 Round 5: 229 peptides, 35 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8532 restraints for refining 3784 atoms. 7791 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2195 (Rfree = 0.000) for 3784 atoms. Found 27 (28 requested) and removed 38 (14 requested) atoms. Cycle 17: After refmac, R = 0.2057 (Rfree = 0.000) for 3747 atoms. Found 24 (28 requested) and removed 23 (14 requested) atoms. Cycle 18: After refmac, R = 0.1780 (Rfree = 0.000) for 3732 atoms. Found 5 (28 requested) and removed 18 (14 requested) atoms. Cycle 19: After refmac, R = 0.1927 (Rfree = 0.000) for 3710 atoms. Found 17 (28 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.1704 (Rfree = 0.000) for 3706 atoms. Found 3 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 3793 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3810 seeds are put forward Round 1: 184 peptides, 40 chains. Longest chain 12 peptides. Score 0.249 Round 2: 199 peptides, 37 chains. Longest chain 13 peptides. Score 0.338 Round 3: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.398 Round 4: 195 peptides, 32 chains. Longest chain 15 peptides. Score 0.391 Round 5: 213 peptides, 37 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 3 Chains 34, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8868 restraints for refining 3791 atoms. 8214 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1990 (Rfree = 0.000) for 3791 atoms. Found 21 (28 requested) and removed 42 (14 requested) atoms. Cycle 22: After refmac, R = 0.1909 (Rfree = 0.000) for 3762 atoms. Found 13 (28 requested) and removed 23 (14 requested) atoms. Cycle 23: After refmac, R = 0.1910 (Rfree = 0.000) for 3743 atoms. Found 23 (28 requested) and removed 23 (14 requested) atoms. Cycle 24: After refmac, R = 0.1863 (Rfree = 0.000) for 3741 atoms. Found 17 (28 requested) and removed 19 (14 requested) atoms. Cycle 25: After refmac, R = 0.1557 (Rfree = 0.000) for 3733 atoms. Found 7 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 3791 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3809 seeds are put forward Round 1: 187 peptides, 40 chains. Longest chain 12 peptides. Score 0.259 Round 2: 210 peptides, 38 chains. Longest chain 14 peptides. Score 0.358 Round 3: 207 peptides, 35 chains. Longest chain 14 peptides. Score 0.388 Round 4: 194 peptides, 32 chains. Longest chain 14 peptides. Score 0.388 Round 5: 194 peptides, 33 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 4 Chains 32, Residues 162, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8788 restraints for refining 3824 atoms. 8135 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2086 (Rfree = 0.000) for 3824 atoms. Found 21 (28 requested) and removed 23 (14 requested) atoms. Cycle 27: After refmac, R = 0.2099 (Rfree = 0.000) for 3802 atoms. Found 20 (28 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.1800 (Rfree = 0.000) for 3792 atoms. Found 12 (28 requested) and removed 17 (14 requested) atoms. Cycle 29: After refmac, R = 0.1842 (Rfree = 0.000) for 3783 atoms. Found 11 (28 requested) and removed 19 (14 requested) atoms. Cycle 30: After refmac, R = 0.1669 (Rfree = 0.000) for 3770 atoms. Found 9 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3813 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3832 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 10 peptides. Score 0.278 Round 2: 205 peptides, 38 chains. Longest chain 10 peptides. Score 0.343 Round 3: 210 peptides, 38 chains. Longest chain 10 peptides. Score 0.358 Round 4: 213 peptides, 36 chains. Longest chain 17 peptides. Score 0.393 Round 5: 207 peptides, 35 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 4 Chains 36, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8659 restraints for refining 3826 atoms. 7987 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1893 (Rfree = 0.000) for 3826 atoms. Found 24 (28 requested) and removed 20 (14 requested) atoms. Cycle 32: After refmac, R = 0.1799 (Rfree = 0.000) for 3819 atoms. Found 22 (28 requested) and removed 20 (14 requested) atoms. Cycle 33: After refmac, R = 0.1744 (Rfree = 0.000) for 3814 atoms. Found 25 (28 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.1738 (Rfree = 0.000) for 3808 atoms. Found 22 (28 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1650 (Rfree = 0.000) for 3809 atoms. Found 22 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 3881 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3908 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 11 peptides. Score 0.264 Round 2: 169 peptides, 31 chains. Longest chain 12 peptides. Score 0.325 Round 3: 184 peptides, 30 chains. Longest chain 11 peptides. Score 0.385 Round 4: 181 peptides, 30 chains. Longest chain 13 peptides. Score 0.376 Round 5: 183 peptides, 30 chains. Longest chain 9 peptides. Score 0.382 Taking the results from Round 3 Chains 30, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8824 restraints for refining 3825 atoms. 8238 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1852 (Rfree = 0.000) for 3825 atoms. Found 27 (28 requested) and removed 16 (14 requested) atoms. Cycle 37: After refmac, R = 0.1743 (Rfree = 0.000) for 3830 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.1412 (Rfree = 0.000) for 3835 atoms. Found 11 (28 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1346 (Rfree = 0.000) for 3827 atoms. Found 6 (28 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.1322 (Rfree = 0.000) for 3816 atoms. Found 7 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3887 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3898 seeds are put forward Round 1: 171 peptides, 37 chains. Longest chain 9 peptides. Score 0.248 Round 2: 176 peptides, 32 chains. Longest chain 12 peptides. Score 0.333 Round 3: 178 peptides, 34 chains. Longest chain 9 peptides. Score 0.312 Round 4: 159 peptides, 28 chains. Longest chain 12 peptides. Score 0.334 Round 5: 173 peptides, 29 chains. Longest chain 13 peptides. Score 0.365 Taking the results from Round 5 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 9117 restraints for refining 3826 atoms. 8570 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1791 (Rfree = 0.000) for 3826 atoms. Found 16 (28 requested) and removed 17 (14 requested) atoms. Cycle 42: After refmac, R = 0.1763 (Rfree = 0.000) for 3821 atoms. Found 19 (28 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.1810 (Rfree = 0.000) for 3823 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. Cycle 44: After refmac, R = 0.1424 (Rfree = 0.000) for 3830 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.1375 (Rfree = 0.000) for 3819 atoms. Found 7 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3879 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3897 seeds are put forward Round 1: 153 peptides, 30 chains. Longest chain 13 peptides. Score 0.286 Round 2: 182 peptides, 32 chains. Longest chain 14 peptides. Score 0.352 Round 3: 184 peptides, 34 chains. Longest chain 14 peptides. Score 0.331 Round 4: 188 peptides, 32 chains. Longest chain 15 peptides. Score 0.370 Round 5: 185 peptides, 32 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 156, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 7444 reflections ( 99.32 % complete ) and 8745 restraints for refining 3824 atoms. 8135 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1758 (Rfree = 0.000) for 3824 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1768 (Rfree = 0.000) for 3806 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1689 (Rfree = 0.000) for 3785 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1695 (Rfree = 0.000) for 3767 atoms. TimeTaking 44.32