Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2glz-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2glz-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2glz-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-parrot-hancs/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 397 and 0 Target number of residues in the AU: 397 Target solvent content: 0.4580 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-2.0-parrot-hancs.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: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.70 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 1 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: 29.894 2.000 Wilson plot Bfac: 15.65 27598 reflections ( 99.95 % complete ) and 0 restraints for refining 2740 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Starting model: R = 0.3264 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2646 (Rfree = 0.000) for 2740 atoms. Found 93 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2787 seeds are put forward Round 1: 252 peptides, 15 chains. Longest chain 50 peptides. Score 0.812 Round 2: 259 peptides, 9 chains. Longest chain 73 peptides. Score 0.868 Round 3: 270 peptides, 10 chains. Longest chain 54 peptides. Score 0.873 Round 4: 280 peptides, 5 chains. Longest chain 105 peptides. Score 0.913 Round 5: 273 peptides, 6 chains. Longest chain 105 peptides. Score 0.901 Taking the results from Round 4 Chains 5, Residues 275, Estimated correctness of the model 99.2 % 5 chains (275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 80 A Built loop between residues 110 A and 116 A Built loop between residues 109 B and 119 B 2 chains (291 residues) following loop building 2 chains (291 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2656 restraints for refining 2755 atoms. 259 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2798 (Rfree = 0.000) for 2755 atoms. Found 90 (94 requested) and removed 52 (47 requested) atoms. Cycle 2: After refmac, R = 0.2345 (Rfree = 0.000) for 2785 atoms. Found 88 (93 requested) and removed 35 (47 requested) atoms. Cycle 3: After refmac, R = 0.2135 (Rfree = 0.000) for 2822 atoms. Found 81 (95 requested) and removed 27 (48 requested) atoms. Cycle 4: After refmac, R = 0.2013 (Rfree = 0.000) for 2870 atoms. Found 59 (96 requested) and removed 39 (49 requested) atoms. Cycle 5: After refmac, R = 0.1924 (Rfree = 0.000) for 2883 atoms. Found 67 (95 requested) and removed 31 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2922 seeds are put forward Round 1: 286 peptides, 5 chains. Longest chain 107 peptides. Score 0.918 Round 2: 288 peptides, 5 chains. Longest chain 142 peptides. Score 0.919 Round 3: 289 peptides, 4 chains. Longest chain 107 peptides. Score 0.925 Round 4: 287 peptides, 6 chains. Longest chain 142 peptides. Score 0.913 Round 5: 289 peptides, 4 chains. Longest chain 107 peptides. Score 0.925 Taking the results from Round 5 Chains 4, Residues 285, Estimated correctness of the model 99.4 % 4 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 79 A Built loop between residues 111 B and 116 B 2 chains (291 residues) following loop building 2 chains (291 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2671 restraints for refining 2826 atoms. 274 conditional restraints added. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2031 (Rfree = 0.000) for 2826 atoms. Found 86 (92 requested) and removed 51 (48 requested) atoms. Cycle 7: After refmac, R = 0.1906 (Rfree = 0.000) for 2855 atoms. Found 88 (92 requested) and removed 24 (49 requested) atoms. Cycle 8: After refmac, R = 0.1831 (Rfree = 0.000) for 2915 atoms. Found 62 (93 requested) and removed 36 (49 requested) atoms. Cycle 9: After refmac, R = 0.1790 (Rfree = 0.000) for 2936 atoms. Found 52 (92 requested) and removed 37 (50 requested) atoms. Cycle 10: After refmac, R = 0.1758 (Rfree = 0.000) for 2946 atoms. Found 75 (91 requested) and removed 34 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2987 seeds are put forward Round 1: 292 peptides, 4 chains. Longest chain 74 peptides. Score 0.927 Round 2: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Round 3: 292 peptides, 4 chains. Longest chain 74 peptides. Score 0.927 Round 4: 292 peptides, 5 chains. Longest chain 148 peptides. Score 0.922 Round 5: 295 peptides, 3 chains. Longest chain 147 peptides. Score 0.934 Taking the results from Round 5 Chains 4, Residues 292, Estimated correctness of the model 99.5 % 3 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 B and 79 B 2 chains (294 residues) following loop building 2 chains (294 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2768 restraints for refining 2976 atoms. 345 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2217 (Rfree = 0.000) for 2976 atoms. Found 83 (91 requested) and removed 95 (50 requested) atoms. Cycle 12: After refmac, R = 0.2012 (Rfree = 0.000) for 2958 atoms. Found 66 (89 requested) and removed 50 (50 requested) atoms. Cycle 13: After refmac, R = 0.1894 (Rfree = 0.000) for 2970 atoms. Found 54 (87 requested) and removed 26 (50 requested) atoms. Cycle 14: After refmac, R = 0.1831 (Rfree = 0.000) for 2994 atoms. Found 44 (88 requested) and removed 23 (51 requested) atoms. Cycle 15: After refmac, R = 0.1796 (Rfree = 0.000) for 3008 atoms. Found 60 (87 requested) and removed 25 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.83 1.64 NCS extension: 3 residues added (143 deleted due to clashes), 3050 seeds are put forward Round 1: 292 peptides, 4 chains. Longest chain 74 peptides. Score 0.927 Round 2: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Round 3: 292 peptides, 4 chains. Longest chain 74 peptides. Score 0.927 Round 4: 293 peptides, 4 chains. Longest chain 148 peptides. Score 0.928 Round 5: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Taking the results from Round 5 Chains 3, Residues 291, Estimated correctness of the model 99.5 % 3 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 79 A 2 chains (293 residues) following loop building 2 chains (293 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2733 restraints for refining 2886 atoms. 318 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1928 (Rfree = 0.000) for 2886 atoms. Found 82 (82 requested) and removed 52 (49 requested) atoms. Cycle 17: After refmac, R = 0.1829 (Rfree = 0.000) for 2910 atoms. Found 66 (81 requested) and removed 28 (49 requested) atoms. Cycle 18: After refmac, R = 0.1764 (Rfree = 0.000) for 2946 atoms. Found 59 (82 requested) and removed 32 (50 requested) atoms. Cycle 19: After refmac, R = 0.1734 (Rfree = 0.000) for 2969 atoms. Found 53 (81 requested) and removed 30 (50 requested) atoms. Cycle 20: After refmac, R = 0.1710 (Rfree = 0.000) for 2989 atoms. Found 52 (80 requested) and removed 38 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 3005 seeds are put forward Round 1: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 2: 292 peptides, 5 chains. Longest chain 110 peptides. Score 0.922 Round 3: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 4: 293 peptides, 4 chains. Longest chain 148 peptides. Score 0.928 Round 5: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Taking the results from Round 5 Chains 3, Residues 291, Estimated correctness of the model 99.5 % 3 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 79 A 2 chains (293 residues) following loop building 2 chains (293 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2705 restraints for refining 2883 atoms. 290 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1912 (Rfree = 0.000) for 2883 atoms. Found 74 (74 requested) and removed 50 (49 requested) atoms. Cycle 22: After refmac, R = 0.1822 (Rfree = 0.000) for 2900 atoms. Found 65 (73 requested) and removed 32 (49 requested) atoms. Cycle 23: After refmac, R = 0.1772 (Rfree = 0.000) for 2929 atoms. Found 70 (74 requested) and removed 27 (50 requested) atoms. Cycle 24: After refmac, R = 0.1745 (Rfree = 0.000) for 2970 atoms. Found 59 (75 requested) and removed 45 (50 requested) atoms. Cycle 25: After refmac, R = 0.1724 (Rfree = 0.000) for 2983 atoms. Found 67 (73 requested) and removed 41 (51 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 3011 seeds are put forward Round 1: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 2: 294 peptides, 4 chains. Longest chain 142 peptides. Score 0.929 Round 3: 293 peptides, 4 chains. Longest chain 148 peptides. Score 0.928 Round 4: 293 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 5: 291 peptides, 3 chains. Longest chain 144 peptides. Score 0.931 Taking the results from Round 4 Chains 3, Residues 290, Estimated correctness of the model 99.5 % 2 chains (286 residues) have been docked in sequence Building loops using Loopy2018 3 chains (290 residues) following loop building 2 chains (286 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2740 restraints for refining 2865 atoms. 362 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1894 (Rfree = 0.000) for 2865 atoms. Found 69 (69 requested) and removed 49 (49 requested) atoms. Cycle 27: After refmac, R = 0.1801 (Rfree = 0.000) for 2882 atoms. Found 67 (67 requested) and removed 28 (49 requested) atoms. Cycle 28: After refmac, R = 0.1763 (Rfree = 0.000) for 2919 atoms. Found 68 (68 requested) and removed 22 (50 requested) atoms. Cycle 29: After refmac, R = 0.1724 (Rfree = 0.000) for 2964 atoms. Found 57 (69 requested) and removed 37 (50 requested) atoms. Cycle 30: After refmac, R = 0.1709 (Rfree = 0.000) for 2978 atoms. Found 67 (67 requested) and removed 32 (51 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.82 1.63 NCS extension: 0 residues added (7 deleted due to clashes), 3016 seeds are put forward Round 1: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 2: 292 peptides, 5 chains. Longest chain 109 peptides. Score 0.922 Round 3: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 4: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 5: 290 peptides, 5 chains. Longest chain 74 peptides. Score 0.921 Taking the results from Round 4 Chains 3, Residues 291, Estimated correctness of the model 99.5 % 2 chains (288 residues) have been docked in sequence Building loops using Loopy2018 3 chains (291 residues) following loop building 2 chains (288 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2738 restraints for refining 2888 atoms. 348 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1890 (Rfree = 0.000) for 2888 atoms. Found 65 (65 requested) and removed 52 (49 requested) atoms. Cycle 32: After refmac, R = 0.1806 (Rfree = 0.000) for 2895 atoms. Found 63 (63 requested) and removed 29 (49 requested) atoms. Cycle 33: After refmac, R = 0.1753 (Rfree = 0.000) for 2925 atoms. Found 64 (64 requested) and removed 25 (50 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1717 (Rfree = 0.000) for 2963 atoms. Found 57 (65 requested) and removed 36 (50 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1710 (Rfree = 0.000) for 2983 atoms. Found 63 (63 requested) and removed 45 (51 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added (147 deleted due to clashes), 3005 seeds are put forward Round 1: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 2: 292 peptides, 4 chains. Longest chain 142 peptides. Score 0.927 Round 3: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Round 4: 292 peptides, 3 chains. Longest chain 147 peptides. Score 0.932 Round 5: 289 peptides, 5 chains. Longest chain 73 peptides. Score 0.920 Taking the results from Round 1 Chains 3, Residues 290, Estimated correctness of the model 99.5 % 3 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 B and 79 B 2 chains (292 residues) following loop building 2 chains (292 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2678 restraints for refining 2875 atoms. 272 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1883 (Rfree = 0.000) for 2875 atoms. Found 59 (59 requested) and removed 52 (49 requested) atoms. Cycle 37: After refmac, R = 0.1789 (Rfree = 0.000) for 2881 atoms. Found 57 (57 requested) and removed 20 (49 requested) atoms. Cycle 38: After refmac, R = 0.1727 (Rfree = 0.000) for 2916 atoms. Found 57 (57 requested) and removed 30 (49 requested) atoms. Cycle 39: After refmac, R = 0.1713 (Rfree = 0.000) for 2942 atoms. Found 56 (56 requested) and removed 30 (50 requested) atoms. Cycle 40: After refmac, R = 0.1708 (Rfree = 0.000) for 2966 atoms. Found 55 (55 requested) and removed 32 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2991 seeds are put forward Round 1: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 2: 292 peptides, 4 chains. Longest chain 142 peptides. Score 0.927 Round 3: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 4: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Round 5: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Taking the results from Round 5 Chains 3, Residues 290, Estimated correctness of the model 99.5 % 3 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 B and 79 B 2 chains (292 residues) following loop building 2 chains (292 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2679 restraints for refining 2865 atoms. 273 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1870 (Rfree = 0.000) for 2865 atoms. Found 51 (51 requested) and removed 50 (49 requested) atoms. Cycle 42: After refmac, R = 0.1766 (Rfree = 0.000) for 2862 atoms. Found 49 (49 requested) and removed 21 (49 requested) atoms. Cycle 43: After refmac, R = 0.1738 (Rfree = 0.000) for 2890 atoms. Found 49 (49 requested) and removed 22 (49 requested) atoms. Cycle 44: After refmac, R = 0.1702 (Rfree = 0.000) for 2916 atoms. Found 49 (49 requested) and removed 25 (49 requested) atoms. Cycle 45: After refmac, R = 0.1669 (Rfree = 0.000) for 2937 atoms. Found 50 (50 requested) and removed 27 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2962 seeds are put forward Round 1: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 2: 287 peptides, 6 chains. Longest chain 107 peptides. Score 0.913 Round 3: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 4: 291 peptides, 4 chains. Longest chain 147 peptides. Score 0.926 Round 5: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 290, Estimated correctness of the model 99.5 % 3 chains (290 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 76 B and 79 B 2 chains (292 residues) following loop building 2 chains (292 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 27598 reflections ( 99.95 % complete ) and 2406 restraints for refining 2348 atoms. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2688 (Rfree = 0.000) for 2348 atoms. Found 40 (40 requested) and removed 0 (40 requested) atoms. Cycle 47: After refmac, R = 0.2441 (Rfree = 0.000) for 2348 atoms. Found 40 (40 requested) and removed 0 (40 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 2348 atoms. Found 41 (41 requested) and removed 2 (41 requested) atoms. Cycle 49: After refmac, R = 0.2218 (Rfree = 0.000) for 2348 atoms. TimeTaking 56.87