Mon 24 Dec 00:38:08 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 2owp-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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/2owp-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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 00:38:13 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/2owp-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.6008 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.2-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.10 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: 29.899 3.200 Wilson plot Bfac: 52.66 Failed to save intermediate PDB 7504 reflections ( 99.15 % complete ) and 0 restraints for refining 2284 atoms. Observations/parameters ratio is 0.82 ------------------------------------------------------ Starting model: R = 0.3420 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2889 (Rfree = 0.000) for 2284 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.44 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward NCS extension: 0 residues added, 2312 seeds are put forward Round 1: 184 peptides, 28 chains. Longest chain 13 peptides. Score 0.459 Round 2: 209 peptides, 22 chains. Longest chain 43 peptides. Score 0.620 Round 3: 202 peptides, 22 chains. Longest chain 23 peptides. Score 0.601 Round 4: 212 peptides, 22 chains. Longest chain 30 peptides. Score 0.628 Round 5: 208 peptides, 24 chains. Longest chain 23 peptides. Score 0.592 Taking the results from Round 4 Chains 22, Residues 190, Estimated correctness of the model 48.4 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3520 restraints for refining 1902 atoms. 2638 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3356 (Rfree = 0.000) for 1902 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 2: After refmac, R = 0.3110 (Rfree = 0.000) for 1858 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.2949 (Rfree = 0.000) for 1837 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2967 (Rfree = 0.000) for 1826 atoms. Found 10 (16 requested) and removed 18 (8 requested) atoms. Cycle 5: After refmac, R = 0.2892 (Rfree = 0.000) for 1812 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.47 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 1882 seeds are put forward Round 1: 207 peptides, 23 chains. Longest chain 29 peptides. Score 0.602 Round 2: 225 peptides, 24 chains. Longest chain 34 peptides. Score 0.637 Round 3: 219 peptides, 21 chains. Longest chain 42 peptides. Score 0.658 Round 4: 209 peptides, 18 chains. Longest chain 28 peptides. Score 0.669 Round 5: 220 peptides, 24 chains. Longest chain 33 peptides. Score 0.624 Taking the results from Round 4 Chains 20, Residues 191, Estimated correctness of the model 58.3 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3490 restraints for refining 1883 atoms. 2580 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3240 (Rfree = 0.000) for 1883 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. Cycle 7: After refmac, R = 0.3019 (Rfree = 0.000) for 1867 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2899 (Rfree = 0.000) for 1861 atoms. Found 2 (16 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2864 (Rfree = 0.000) for 1843 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2813 (Rfree = 0.000) for 1834 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.46 Search for helices and strands: 0 residues in 0 chains, 1900 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 1936 seeds are put forward Round 1: 204 peptides, 24 chains. Longest chain 23 peptides. Score 0.580 Round 2: 212 peptides, 23 chains. Longest chain 23 peptides. Score 0.616 Round 3: 207 peptides, 19 chains. Longest chain 27 peptides. Score 0.652 Round 4: 220 peptides, 22 chains. Longest chain 26 peptides. Score 0.649 Round 5: 209 peptides, 18 chains. Longest chain 30 peptides. Score 0.669 Taking the results from Round 5 Chains 20, Residues 191, Estimated correctness of the model 58.3 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3690 restraints for refining 1883 atoms. 2860 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3227 (Rfree = 0.000) for 1883 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.3080 (Rfree = 0.000) for 1877 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.3011 (Rfree = 0.000) for 1867 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2976 (Rfree = 0.000) for 1857 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2933 (Rfree = 0.000) for 1844 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.48 Search for helices and strands: 0 residues in 0 chains, 1890 seeds are put forward NCS extension: 39 residues added (10 deleted due to clashes), 1929 seeds are put forward Round 1: 208 peptides, 24 chains. Longest chain 26 peptides. Score 0.592 Round 2: 220 peptides, 23 chains. Longest chain 26 peptides. Score 0.637 Round 3: 205 peptides, 21 chains. Longest chain 25 peptides. Score 0.622 Round 4: 219 peptides, 21 chains. Longest chain 27 peptides. Score 0.658 Round 5: 208 peptides, 19 chains. Longest chain 27 peptides. Score 0.654 Taking the results from Round 4 Chains 21, Residues 198, Estimated correctness of the model 55.7 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3639 restraints for refining 1883 atoms. 2764 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3270 (Rfree = 0.000) for 1883 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.3119 (Rfree = 0.000) for 1887 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.3036 (Rfree = 0.000) for 1880 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2983 (Rfree = 0.000) for 1870 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2946 (Rfree = 0.000) for 1863 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 1937 seeds are put forward Round 1: 215 peptides, 23 chains. Longest chain 26 peptides. Score 0.624 Round 2: 211 peptides, 20 chains. Longest chain 27 peptides. Score 0.650 Round 3: 213 peptides, 21 chains. Longest chain 37 peptides. Score 0.643 Round 4: 207 peptides, 20 chains. Longest chain 29 peptides. Score 0.640 Round 5: 215 peptides, 23 chains. Longest chain 29 peptides. Score 0.624 Taking the results from Round 2 Chains 24, Residues 191, Estimated correctness of the model 53.8 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3491 restraints for refining 1883 atoms. 2557 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3085 (Rfree = 0.000) for 1883 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2959 (Rfree = 0.000) for 1878 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2882 (Rfree = 0.000) for 1869 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2812 (Rfree = 0.000) for 1862 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2773 (Rfree = 0.000) for 1855 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 2.41 Search for helices and strands: 0 residues in 0 chains, 1902 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 1919 seeds are put forward Round 1: 215 peptides, 24 chains. Longest chain 24 peptides. Score 0.611 Round 2: 212 peptides, 21 chains. Longest chain 25 peptides. Score 0.640 Round 3: 220 peptides, 22 chains. Longest chain 26 peptides. Score 0.649 Round 4: 224 peptides, 23 chains. Longest chain 25 peptides. Score 0.647 Round 5: 223 peptides, 25 chains. Longest chain 19 peptides. Score 0.620 Taking the results from Round 3 Chains 24, Residues 198, Estimated correctness of the model 53.6 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3756 restraints for refining 1884 atoms. 2917 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2956 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2862 (Rfree = 0.000) for 1881 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2791 (Rfree = 0.000) for 1879 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2761 (Rfree = 0.000) for 1870 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 30: After refmac, R = 0.2722 (Rfree = 0.000) for 1864 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.44 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 1957 seeds are put forward Round 1: 218 peptides, 20 chains. Longest chain 25 peptides. Score 0.667 Round 2: 215 peptides, 19 chains. Longest chain 35 peptides. Score 0.672 Round 3: 217 peptides, 23 chains. Longest chain 24 peptides. Score 0.629 Round 4: 218 peptides, 21 chains. Longest chain 32 peptides. Score 0.655 Round 5: 223 peptides, 20 chains. Longest chain 29 peptides. Score 0.679 Taking the results from Round 5 Chains 24, Residues 203, Estimated correctness of the model 60.6 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3268 restraints for refining 1884 atoms. 2261 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3170 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2962 (Rfree = 0.000) for 1881 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2847 (Rfree = 0.000) for 1875 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2782 (Rfree = 0.000) for 1872 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2732 (Rfree = 0.000) for 1868 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.42 Search for helices and strands: 0 residues in 0 chains, 1924 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1942 seeds are put forward Round 1: 195 peptides, 18 chains. Longest chain 24 peptides. Score 0.633 Round 2: 205 peptides, 18 chains. Longest chain 25 peptides. Score 0.659 Round 3: 207 peptides, 18 chains. Longest chain 32 peptides. Score 0.664 Round 4: 207 peptides, 19 chains. Longest chain 34 peptides. Score 0.652 Round 5: 222 peptides, 23 chains. Longest chain 38 peptides. Score 0.642 Taking the results from Round 3 Chains 21, Residues 189, Estimated correctness of the model 57.2 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3539 restraints for refining 1884 atoms. 2630 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3113 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.2877 (Rfree = 0.000) for 1887 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2769 (Rfree = 0.000) for 1882 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2717 (Rfree = 0.000) for 1876 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2710 (Rfree = 0.000) for 1865 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 1916 seeds are put forward NCS extension: 65 residues added (0 deleted due to clashes), 1981 seeds are put forward Round 1: 189 peptides, 20 chains. Longest chain 29 peptides. Score 0.591 Round 2: 196 peptides, 18 chains. Longest chain 30 peptides. Score 0.636 Round 3: 195 peptides, 21 chains. Longest chain 28 peptides. Score 0.594 Round 4: 194 peptides, 18 chains. Longest chain 24 peptides. Score 0.631 Round 5: 197 peptides, 21 chains. Longest chain 20 peptides. Score 0.600 Taking the results from Round 2 Chains 18, Residues 178, Estimated correctness of the model 50.4 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3230 restraints for refining 1890 atoms. 2215 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3039 (Rfree = 0.000) for 1890 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2838 (Rfree = 0.000) for 1881 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2819 (Rfree = 0.000) for 1870 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.2858 (Rfree = 0.000) for 1863 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.2822 (Rfree = 0.000) for 1855 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 1920 seeds are put forward NCS extension: 30 residues added (7 deleted due to clashes), 1950 seeds are put forward Round 1: 196 peptides, 27 chains. Longest chain 21 peptides. Score 0.514 Round 2: 203 peptides, 20 chains. Longest chain 33 peptides. Score 0.629 Round 3: 195 peptides, 20 chains. Longest chain 35 peptides. Score 0.608 Round 4: 203 peptides, 21 chains. Longest chain 30 peptides. Score 0.616 Round 5: 195 peptides, 19 chains. Longest chain 40 peptides. Score 0.620 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 183, Estimated correctness of the model 48.6 % 2 chains (35 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2owp-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (183 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7504 reflections ( 99.15 % complete ) and 3561 restraints for refining 1884 atoms. 2705 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2954 (Rfree = 0.000) for 1884 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2827 (Rfree = 0.000) for 1867 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2787 (Rfree = 0.000) for 1855 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2797 (Rfree = 0.000) for 1844 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 35.17