null Mon 24 Dec 08:07:48 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 2oyo-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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/2oyo-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 08:07:52 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/2oyo-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 260 and 0 Target number of residues in the AU: 260 Target solvent content: 0.6636 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-3.8-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 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: 83.295 3.800 Wilson plot Bfac: 87.04 4247 reflections ( 99.79 % complete ) and 0 restraints for refining 3458 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3249 (Rfree = 0.000) for 3458 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 0 residues added, 3560 seeds are put forward Round 1: 143 peptides, 26 chains. Longest chain 11 peptides. Score 0.344 Round 2: 163 peptides, 28 chains. Longest chain 10 peptides. Score 0.390 Round 3: 174 peptides, 24 chains. Longest chain 22 peptides. Score 0.495 Round 4: 179 peptides, 24 chains. Longest chain 16 peptides. Score 0.512 Round 5: 178 peptides, 24 chains. Longest chain 12 peptides. Score 0.509 Taking the results from Round 4 Chains 25, Residues 155, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6652 restraints for refining 2835 atoms. 5969 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2253 (Rfree = 0.000) for 2835 atoms. Found 12 (15 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2015 (Rfree = 0.000) for 2785 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.1957 (Rfree = 0.000) for 2772 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.1931 (Rfree = 0.000) for 2765 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.1907 (Rfree = 0.000) for 2754 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2911 seeds are put forward Round 1: 170 peptides, 32 chains. Longest chain 12 peptides. Score 0.350 Round 2: 194 peptides, 29 chains. Longest chain 15 peptides. Score 0.488 Round 3: 192 peptides, 29 chains. Longest chain 13 peptides. Score 0.481 Round 4: 190 peptides, 26 chains. Longest chain 16 peptides. Score 0.519 Round 5: 183 peptides, 26 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 4 Chains 26, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6545 restraints for refining 2803 atoms. 5915 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2104 (Rfree = 0.000) for 2803 atoms. Found 13 (15 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.2065 (Rfree = 0.000) for 2774 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. Cycle 8: After refmac, R = 0.2082 (Rfree = 0.000) for 2754 atoms. Found 11 (15 requested) and removed 19 (7 requested) atoms. Cycle 9: After refmac, R = 0.1813 (Rfree = 0.000) for 2736 atoms. Found 7 (15 requested) and removed 16 (7 requested) atoms. Cycle 10: After refmac, R = 0.1527 (Rfree = 0.000) for 2723 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2890 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2906 seeds are put forward Round 1: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.367 Round 2: 181 peptides, 27 chains. Longest chain 11 peptides. Score 0.473 Round 3: 186 peptides, 26 chains. Longest chain 19 peptides. Score 0.506 Round 4: 186 peptides, 31 chains. Longest chain 13 peptides. Score 0.428 Round 5: 195 peptides, 27 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 5 Chains 29, Residues 168, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6667 restraints for refining 2835 atoms. 5993 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1920 (Rfree = 0.000) for 2835 atoms. Found 12 (15 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.1933 (Rfree = 0.000) for 2816 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.1965 (Rfree = 0.000) for 2800 atoms. Found 12 (15 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.1467 (Rfree = 0.000) for 2782 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1453 (Rfree = 0.000) for 2773 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2909 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2921 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 10 peptides. Score 0.350 Round 2: 184 peptides, 31 chains. Longest chain 11 peptides. Score 0.420 Round 3: 175 peptides, 26 chains. Longest chain 16 peptides. Score 0.467 Round 4: 181 peptides, 26 chains. Longest chain 13 peptides. Score 0.488 Round 5: 178 peptides, 27 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 4 Chains 26, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6775 restraints for refining 2836 atoms. 6181 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1934 (Rfree = 0.000) for 2836 atoms. Found 5 (15 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.1830 (Rfree = 0.000) for 2805 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.1763 (Rfree = 0.000) for 2790 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.1721 (Rfree = 0.000) for 2775 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1403 (Rfree = 0.000) for 2766 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 2904 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2915 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 9 peptides. Score 0.303 Round 2: 173 peptides, 28 chains. Longest chain 12 peptides. Score 0.428 Round 3: 179 peptides, 28 chains. Longest chain 13 peptides. Score 0.450 Round 4: 189 peptides, 28 chains. Longest chain 17 peptides. Score 0.486 Round 5: 179 peptides, 26 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 4 Chains 28, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6640 restraints for refining 2836 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1933 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.1887 (Rfree = 0.000) for 2825 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.1790 (Rfree = 0.000) for 2824 atoms. Found 8 (15 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1403 (Rfree = 0.000) for 2810 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1502 (Rfree = 0.000) for 2802 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2966 seeds are put forward Round 1: 148 peptides, 28 chains. Longest chain 17 peptides. Score 0.329 Round 2: 173 peptides, 27 chains. Longest chain 15 peptides. Score 0.444 Round 3: 159 peptides, 28 chains. Longest chain 20 peptides. Score 0.374 Round 4: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.426 Round 5: 169 peptides, 25 chains. Longest chain 16 peptides. Score 0.462 Taking the results from Round 5 Chains 25, Residues 144, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6651 restraints for refining 2836 atoms. 6059 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1951 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2056 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2040 (Rfree = 0.000) for 2813 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 29: After refmac, R = 0.1979 (Rfree = 0.000) for 2800 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.1446 (Rfree = 0.000) for 2789 atoms. Found 5 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2903 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2929 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 8 peptides. Score 0.280 Round 2: 161 peptides, 29 chains. Longest chain 13 peptides. Score 0.365 Round 3: 159 peptides, 30 chains. Longest chain 10 peptides. Score 0.339 Round 4: 165 peptides, 29 chains. Longest chain 13 peptides. Score 0.381 Round 5: 163 peptides, 28 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 5 Chains 28, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6842 restraints for refining 2836 atoms. 6330 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1996 (Rfree = 0.000) for 2836 atoms. Found 12 (15 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.1842 (Rfree = 0.000) for 2817 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.1815 (Rfree = 0.000) for 2802 atoms. Found 13 (15 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.1733 (Rfree = 0.000) for 2799 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1571 (Rfree = 0.000) for 2797 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.64 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2955 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 11 peptides. Score 0.265 Round 2: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.385 Round 3: 135 peptides, 24 chains. Longest chain 10 peptides. Score 0.347 Round 4: 137 peptides, 23 chains. Longest chain 12 peptides. Score 0.373 Round 5: 141 peptides, 24 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 2 Chains 23, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6686 restraints for refining 2772 atoms. 6241 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1664 (Rfree = 0.000) for 2772 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.1598 (Rfree = 0.000) for 2766 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1563 (Rfree = 0.000) for 2760 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.1635 (Rfree = 0.000) for 2750 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1275 (Rfree = 0.000) for 2746 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 2863 seeds are put forward NCS extension: 0 residues added, 2863 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 8 peptides. Score 0.226 Round 2: 131 peptides, 21 chains. Longest chain 16 peptides. Score 0.384 Round 3: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.343 Round 4: 133 peptides, 23 chains. Longest chain 14 peptides. Score 0.357 Round 5: 141 peptides, 26 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 2 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6409 restraints for refining 2723 atoms. 5990 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1612 (Rfree = 0.000) for 2723 atoms. Found 12 (14 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.1612 (Rfree = 0.000) for 2708 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.1564 (Rfree = 0.000) for 2704 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.1485 (Rfree = 0.000) for 2702 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 45: After refmac, R = 0.1399 (Rfree = 0.000) for 2693 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2839 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 7 peptides. Score 0.240 Round 2: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.323 Round 3: 132 peptides, 25 chains. Longest chain 11 peptides. Score 0.316 Round 4: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.345 Round 5: 139 peptides, 26 chains. Longest chain 12 peptides. Score 0.327 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 114, 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 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4247 reflections ( 99.79 % complete ) and 6399 restraints for refining 2744 atoms. 5968 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1929 (Rfree = 0.000) for 2744 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1573 (Rfree = 0.000) for 2723 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1496 (Rfree = 0.000) for 2712 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1542 (Rfree = 0.000) for 2702 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:05 GMT 2018 Job finished. TimeTaking 36.29 Used memory is bytes: 19938952