Mon 24 Dec 00:57:15 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 2glz-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-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/2glz-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-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 00:57:19 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/2glz-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-2.0-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 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-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: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-2.0-parrot-mrncs.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 2724 atoms. Observations/parameters ratio is 2.53 ------------------------------------------------------ Starting model: R = 0.3296 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2689 (Rfree = 0.000) for 2724 atoms. Found 93 (93 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.82 1.63 NCS extension: 0 residues added, 2767 seeds are put forward Round 1: 262 peptides, 20 chains. Longest chain 28 peptides. Score 0.786 Round 2: 276 peptides, 10 chains. Longest chain 57 peptides. Score 0.880 Round 3: 278 peptides, 7 chains. Longest chain 65 peptides. Score 0.900 Round 4: 288 peptides, 4 chains. Longest chain 107 peptides. Score 0.924 Round 5: 289 peptides, 4 chains. Longest chain 142 peptides. Score 0.925 Taking the results from Round 5 Chains 4, Residues 285, Estimated correctness of the model 99.4 % 3 chains (282 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 118 A 3 chains (291 residues) following loop building 2 chains (288 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2755 restraints for refining 2786 atoms. 365 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 2786 atoms. Found 90 (95 requested) and removed 53 (47 requested) atoms. Cycle 2: After refmac, R = 0.2395 (Rfree = 0.000) for 2819 atoms. Found 77 (94 requested) and removed 47 (48 requested) atoms. Cycle 3: After refmac, R = 0.2206 (Rfree = 0.000) for 2836 atoms. Found 78 (93 requested) and removed 31 (48 requested) atoms. Cycle 4: After refmac, R = 0.2057 (Rfree = 0.000) for 2875 atoms. Found 68 (94 requested) and removed 28 (49 requested) atoms. Cycle 5: After refmac, R = 0.1952 (Rfree = 0.000) for 2909 atoms. Found 72 (95 requested) and removed 29 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.84 1.65 NCS extension: 5 residues added (145 deleted due to clashes), 2963 seeds are put forward Round 1: 290 peptides, 5 chains. Longest chain 74 peptides. Score 0.921 Round 2: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 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: 295 peptides, 2 chains. Longest chain 148 peptides. Score 0.939 Taking the results from Round 5 Chains 2, Residues 293, Estimated correctness of the model 99.6 % 2 chains (293 residues) have been docked in sequence Building loops using Loopy2018 2 chains (293 residues) following loop building 2 chains (293 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2681 restraints for refining 2841 atoms. 266 conditional restraints added. Observations/parameters ratio is 2.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2015 (Rfree = 0.000) for 2841 atoms. Found 93 (93 requested) and removed 52 (48 requested) atoms. Cycle 7: After refmac, R = 0.1911 (Rfree = 0.000) for 2879 atoms. Found 74 (92 requested) and removed 41 (49 requested) atoms. Cycle 8: After refmac, R = 0.1825 (Rfree = 0.000) for 2908 atoms. Found 77 (91 requested) and removed 35 (49 requested) atoms. Cycle 9: After refmac, R = 0.1800 (Rfree = 0.000) for 2949 atoms. Found 67 (93 requested) and removed 50 (50 requested) atoms. Cycle 10: After refmac, R = 0.1767 (Rfree = 0.000) for 2962 atoms. Found 77 (91 requested) and removed 45 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 2996 seeds are put forward Round 1: 293 peptides, 4 chains. Longest chain 148 peptides. Score 0.928 Round 2: 293 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 3: 289 peptides, 4 chains. Longest chain 74 peptides. Score 0.925 Round 4: 293 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 Round 5: 290 peptides, 3 chains. Longest chain 148 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 2789 restraints for refining 2866 atoms. 411 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1917 (Rfree = 0.000) for 2866 atoms. Found 86 (86 requested) and removed 51 (49 requested) atoms. Cycle 12: After refmac, R = 0.1816 (Rfree = 0.000) for 2898 atoms. Found 62 (85 requested) and removed 35 (49 requested) atoms. Cycle 13: After refmac, R = 0.1771 (Rfree = 0.000) for 2923 atoms. Found 83 (84 requested) and removed 36 (50 requested) atoms. Cycle 14: After refmac, R = 0.1758 (Rfree = 0.000) for 2968 atoms. Found 57 (85 requested) and removed 50 (50 requested) atoms. Cycle 15: After refmac, R = 0.1730 (Rfree = 0.000) for 2972 atoms. Found 74 (83 requested) and removed 38 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added (7 deleted due to clashes), 3010 seeds are put forward Round 1: 294 peptides, 4 chains. Longest chain 148 peptides. Score 0.929 Round 2: 292 peptides, 4 chains. Longest chain 140 peptides. Score 0.927 Round 3: 293 peptides, 4 chains. Longest chain 148 peptides. Score 0.928 Round 4: 294 peptides, 3 chains. Longest chain 148 peptides. Score 0.933 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 B and 79 B 2 chains (293 residues) following loop building 2 chains (293 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2675 restraints for refining 2860 atoms. 260 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1912 (Rfree = 0.000) for 2860 atoms. Found 78 (78 requested) and removed 50 (48 requested) atoms. Cycle 17: After refmac, R = 0.1804 (Rfree = 0.000) for 2887 atoms. Found 76 (76 requested) and removed 24 (49 requested) atoms. Cycle 18: After refmac, R = 0.1754 (Rfree = 0.000) for 2938 atoms. Found 60 (78 requested) and removed 34 (50 requested) atoms. Cycle 19: After refmac, R = 0.1722 (Rfree = 0.000) for 2962 atoms. Found 58 (77 requested) and removed 33 (50 requested) atoms. Cycle 20: After refmac, R = 0.1691 (Rfree = 0.000) for 2985 atoms. Found 64 (75 requested) and removed 37 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.83 1.64 NCS extension: 0 residues added, 3016 seeds are put forward Round 1: 295 peptides, 3 chains. Longest chain 149 peptides. Score 0.934 Round 2: 293 peptides, 4 chains. Longest chain 140 peptides. Score 0.928 Round 3: 294 peptides, 4 chains. Longest chain 149 peptides. Score 0.929 Round 4: 294 peptides, 3 chains. Longest chain 149 peptides. Score 0.933 Round 5: 280 peptides, 7 chains. Longest chain 73 peptides. Score 0.902 Taking the results from Round 1 Chains 3, Residues 292, Estimated correctness of the model 99.5 % 3 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 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 2684 restraints for refining 2876 atoms. 262 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1880 (Rfree = 0.000) for 2876 atoms. Found 71 (71 requested) and removed 50 (49 requested) atoms. Cycle 22: After refmac, R = 0.1783 (Rfree = 0.000) for 2895 atoms. Found 69 (69 requested) and removed 19 (49 requested) atoms. Cycle 23: After refmac, R = 0.1739 (Rfree = 0.000) for 2945 atoms. Found 59 (70 requested) and removed 34 (50 requested) atoms. Cycle 24: After refmac, R = 0.1724 (Rfree = 0.000) for 2968 atoms. Found 65 (69 requested) and removed 33 (50 requested) atoms. Cycle 25: After refmac, R = 0.1695 (Rfree = 0.000) for 2997 atoms. Found 67 (67 requested) and removed 41 (51 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.84 1.65 NCS extension: 0 residues added, 3024 seeds are put forward Round 1: 295 peptides, 3 chains. Longest chain 149 peptides. Score 0.934 Round 2: 293 peptides, 4 chains. Longest chain 140 peptides. Score 0.928 Round 3: 294 peptides, 4 chains. Longest chain 149 peptides. Score 0.929 Round 4: 294 peptides, 3 chains. Longest chain 149 peptides. Score 0.933 Round 5: 294 peptides, 4 chains. Longest chain 75 peptides. Score 0.929 Taking the results from Round 1 Chains 3, Residues 292, Estimated correctness of the model 99.5 % 3 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 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 2693 restraints for refining 2877 atoms. 271 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1876 (Rfree = 0.000) for 2877 atoms. Found 63 (63 requested) and removed 49 (49 requested) atoms. Cycle 27: After refmac, R = 0.1773 (Rfree = 0.000) for 2889 atoms. Found 61 (61 requested) and removed 24 (49 requested) atoms. Cycle 28: After refmac, R = 0.1730 (Rfree = 0.000) for 2925 atoms. Found 62 (62 requested) and removed 30 (50 requested) atoms. Cycle 29: After refmac, R = 0.1712 (Rfree = 0.000) for 2956 atoms. Found 60 (63 requested) and removed 37 (50 requested) atoms. Cycle 30: After refmac, R = 0.1688 (Rfree = 0.000) for 2977 atoms. Found 61 (61 requested) and removed 33 (51 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.84 1.65 NCS extension: 2 residues added (145 deleted due to clashes), 3010 seeds are put forward Round 1: 293 peptides, 3 chains. Longest chain 146 peptides. Score 0.933 Round 2: 294 peptides, 4 chains. Longest chain 149 peptides. Score 0.929 Round 3: 295 peptides, 3 chains. Longest chain 147 peptides. Score 0.934 Round 4: 295 peptides, 3 chains. Longest chain 149 peptides. Score 0.934 Round 5: 294 peptides, 4 chains. Longest chain 75 peptides. Score 0.929 Taking the results from Round 4 Chains 3, Residues 292, Estimated correctness of the model 99.5 % 2 chains (289 residues) have been docked in sequence Building loops using Loopy2018 3 chains (292 residues) following loop building 2 chains (289 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2749 restraints for refining 2877 atoms. 352 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1873 (Rfree = 0.000) for 2877 atoms. Found 57 (57 requested) and removed 49 (49 requested) atoms. Cycle 32: After refmac, R = 0.1770 (Rfree = 0.000) for 2882 atoms. Found 55 (55 requested) and removed 22 (49 requested) atoms. Cycle 33: After refmac, R = 0.1727 (Rfree = 0.000) for 2914 atoms. Found 55 (55 requested) and removed 16 (49 requested) atoms. Cycle 34: After refmac, R = 0.1696 (Rfree = 0.000) for 2953 atoms. Found 54 (57 requested) and removed 37 (50 requested) atoms. Cycle 35: After refmac, R = 0.1680 (Rfree = 0.000) for 2967 atoms. Found 55 (55 requested) and removed 35 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.84 1.65 NCS extension: 2 residues added (145 deleted due to clashes), 2992 seeds are put forward Round 1: 295 peptides, 2 chains. Longest chain 148 peptides. Score 0.939 Round 2: 290 peptides, 6 chains. Longest chain 74 peptides. Score 0.916 Round 3: 295 peptides, 2 chains. Longest chain 148 peptides. Score 0.939 Round 4: 292 peptides, 4 chains. Longest chain 142 peptides. Score 0.927 Round 5: 292 peptides, 4 chains. Longest chain 148 peptides. Score 0.927 Taking the results from Round 3 Chains 2, Residues 293, Estimated correctness of the model 99.6 % 2 chains (293 residues) have been docked in sequence Building loops using Loopy2018 2 chains (293 residues) following loop building 2 chains (293 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2718 restraints for refining 2886 atoms. 305 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1876 (Rfree = 0.000) for 2886 atoms. Found 51 (51 requested) and removed 49 (49 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 2883 atoms. Found 49 (49 requested) and removed 24 (49 requested) atoms. Cycle 38: After refmac, R = 0.1717 (Rfree = 0.000) for 2908 atoms. Found 49 (49 requested) and removed 19 (49 requested) atoms. Cycle 39: After refmac, R = 0.1682 (Rfree = 0.000) for 2937 atoms. Found 50 (50 requested) and removed 23 (50 requested) atoms. Cycle 40: After refmac, R = 0.1687 (Rfree = 0.000) for 2962 atoms. Found 50 (50 requested) and removed 32 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.83 1.64 NCS extension: 2 residues added (145 deleted due to clashes), 2985 seeds are put forward Round 1: 293 peptides, 4 chains. Longest chain 147 peptides. Score 0.928 Round 2: 291 peptides, 4 chains. Longest chain 140 peptides. Score 0.926 Round 3: 293 peptides, 3 chains. Longest chain 147 peptides. Score 0.933 Round 4: 291 peptides, 4 chains. Longest chain 140 peptides. Score 0.926 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 A and 79 A 2 chains (292 residues) following loop building 2 chains (292 residues) in sequence following loop building ------------------------------------------------------ 27598 reflections ( 99.95 % complete ) and 2721 restraints for refining 2878 atoms. 315 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1876 (Rfree = 0.000) for 2878 atoms. Found 49 (49 requested) and removed 51 (49 requested) atoms. Cycle 42: After refmac, R = 0.1779 (Rfree = 0.000) for 2873 atoms. Found 49 (49 requested) and removed 18 (49 requested) atoms. Cycle 43: After refmac, R = 0.1738 (Rfree = 0.000) for 2903 atoms. Found 49 (49 requested) and removed 19 (49 requested) atoms. Cycle 44: After refmac, R = 0.1719 (Rfree = 0.000) for 2932 atoms. Found 50 (50 requested) and removed 30 (50 requested) atoms. Cycle 45: After refmac, R = 0.1709 (Rfree = 0.000) for 2949 atoms. Found 50 (50 requested) and removed 27 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.84 1.65 NCS extension: 3 residues added (144 deleted due to clashes), 2977 seeds are put forward Round 1: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Round 2: 290 peptides, 5 chains. Longest chain 74 peptides. Score 0.921 Round 3: 291 peptides, 3 chains. Longest chain 147 peptides. Score 0.931 Round 4: 291 peptides, 4 chains. Longest chain 147 peptides. Score 0.926 Round 5: 292 peptides, 4 chains. Longest chain 147 peptides. Score 0.927 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 288, Estimated correctness of the model 99.5 % 3 chains (288 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 110 B and 115 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 = 0.2671 (Rfree = 0.000) for 2348 atoms. Found 40 (40 requested) and removed 0 (40 requested) atoms. Cycle 47: After refmac, R = 0.2433 (Rfree = 0.000) for 2348 atoms. Found 40 (40 requested) and removed 0 (40 requested) atoms. Cycle 48: After refmac, R = 0.2332 (Rfree = 0.000) for 2348 atoms. Found 41 (41 requested) and removed 2 (41 requested) atoms. Cycle 49: After refmac, R = 0.2231 (Rfree = 0.000) for 2348 atoms. TimeTaking 40.28