null Mon 24 Dec 08:07:12 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 2fur-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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/2fur-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 08:07:16 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/2fur-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.6674 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 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 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: 55.473 3.800 Wilson plot Bfac: 89.68 4300 reflections ( 99.54 % complete ) and 0 restraints for refining 3702 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3378 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2442 (Rfree = 0.000) for 3702 atoms. Found 16 (20 requested) and removed 47 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 0 residues added, 3750 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 8 peptides. Score 0.322 Round 2: 194 peptides, 30 chains. Longest chain 19 peptides. Score 0.479 Round 3: 216 peptides, 33 chains. Longest chain 13 peptides. Score 0.510 Round 4: 220 peptides, 28 chains. Longest chain 19 peptides. Score 0.593 Round 5: 236 peptides, 32 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Chains 28, Residues 192, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7017 restraints for refining 3022 atoms. 6255 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2335 (Rfree = 0.000) for 3022 atoms. Found 8 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2129 (Rfree = 0.000) for 2973 atoms. Found 3 (16 requested) and removed 24 (8 requested) atoms. Cycle 3: After refmac, R = 0.2203 (Rfree = 0.000) for 2927 atoms. Found 2 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2076 (Rfree = 0.000) for 2906 atoms. Found 5 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2116 (Rfree = 0.000) for 2882 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3031 seeds are put forward Round 1: 181 peptides, 35 chains. Longest chain 11 peptides. Score 0.347 Round 2: 201 peptides, 32 chains. Longest chain 13 peptides. Score 0.473 Round 3: 220 peptides, 33 chains. Longest chain 16 peptides. Score 0.523 Round 4: 218 peptides, 30 chains. Longest chain 15 peptides. Score 0.559 Round 5: 225 peptides, 33 chains. Longest chain 17 peptides. Score 0.539 Taking the results from Round 4 Chains 30, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 6882 restraints for refining 2916 atoms. 6160 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2379 (Rfree = 0.000) for 2916 atoms. Found 6 (16 requested) and removed 23 (8 requested) atoms. Cycle 7: After refmac, R = 0.2078 (Rfree = 0.000) for 2878 atoms. Found 1 (15 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2020 (Rfree = 0.000) for 2855 atoms. Found 0 (15 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.1964 (Rfree = 0.000) for 2843 atoms. Found 0 (15 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.1942 (Rfree = 0.000) for 2830 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 4.09 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2948 seeds are put forward Round 1: 207 peptides, 37 chains. Longest chain 14 peptides. Score 0.416 Round 2: 222 peptides, 32 chains. Longest chain 18 peptides. Score 0.544 Round 3: 227 peptides, 29 chains. Longest chain 17 peptides. Score 0.600 Round 4: 228 peptides, 31 chains. Longest chain 20 peptides. Score 0.577 Round 5: 245 peptides, 29 chains. Longest chain 24 peptides. Score 0.650 Taking the results from Round 5 Chains 29, Residues 216, Estimated correctness of the model 20.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7054 restraints for refining 3024 atoms. 6219 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2446 (Rfree = 0.000) for 3024 atoms. Found 7 (16 requested) and removed 23 (8 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 2991 atoms. Found 2 (16 requested) and removed 18 (8 requested) atoms. Cycle 13: After refmac, R = 0.2244 (Rfree = 0.000) for 2965 atoms. Found 5 (16 requested) and removed 15 (8 requested) atoms. Cycle 14: After refmac, R = 0.2133 (Rfree = 0.000) for 2952 atoms. Found 1 (16 requested) and removed 16 (8 requested) atoms. Cycle 15: After refmac, R = 0.2184 (Rfree = 0.000) for 2935 atoms. Found 3 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 3032 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3050 seeds are put forward Round 1: 165 peptides, 33 chains. Longest chain 11 peptides. Score 0.315 Round 2: 199 peptides, 30 chains. Longest chain 16 peptides. Score 0.496 Round 3: 182 peptides, 28 chains. Longest chain 17 peptides. Score 0.467 Round 4: 201 peptides, 28 chains. Longest chain 19 peptides. Score 0.533 Round 5: 213 peptides, 27 chains. Longest chain 35 peptides. Score 0.585 Taking the results from Round 5 Chains 28, Residues 186, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7040 restraints for refining 3023 atoms. 6280 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2442 (Rfree = 0.000) for 3023 atoms. Found 13 (16 requested) and removed 24 (8 requested) atoms. Cycle 17: After refmac, R = 0.2115 (Rfree = 0.000) for 3000 atoms. Found 1 (16 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 2978 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 2958 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.1969 (Rfree = 0.000) for 2946 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 3040 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3060 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 13 peptides. Score 0.349 Round 2: 198 peptides, 28 chains. Longest chain 20 peptides. Score 0.523 Round 3: 198 peptides, 29 chains. Longest chain 26 peptides. Score 0.508 Round 4: 209 peptides, 32 chains. Longest chain 16 peptides. Score 0.501 Round 5: 213 peptides, 31 chains. Longest chain 16 peptides. Score 0.529 Taking the results from Round 5 Chains 31, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7272 restraints for refining 3024 atoms. 6575 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2368 (Rfree = 0.000) for 3024 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2144 (Rfree = 0.000) for 3010 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2019 (Rfree = 0.000) for 2995 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.1962 (Rfree = 0.000) for 2984 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 2967 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 3050 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3069 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 12 peptides. Score 0.305 Round 2: 188 peptides, 27 chains. Longest chain 13 peptides. Score 0.504 Round 3: 178 peptides, 25 chains. Longest chain 14 peptides. Score 0.500 Round 4: 186 peptides, 25 chains. Longest chain 15 peptides. Score 0.528 Round 5: 207 peptides, 28 chains. Longest chain 15 peptides. Score 0.553 Taking the results from Round 5 Chains 29, Residues 179, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7072 restraints for refining 3024 atoms. 6326 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2359 (Rfree = 0.000) for 3024 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 3011 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2001 (Rfree = 0.000) for 3004 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1928 (Rfree = 0.000) for 2990 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1917 (Rfree = 0.000) for 2974 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3088 seeds are put forward Round 1: 149 peptides, 30 chains. Longest chain 11 peptides. Score 0.301 Round 2: 175 peptides, 25 chains. Longest chain 16 peptides. Score 0.490 Round 3: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.436 Round 4: 190 peptides, 29 chains. Longest chain 14 peptides. Score 0.480 Round 5: 190 peptides, 25 chains. Longest chain 14 peptides. Score 0.541 Taking the results from Round 5 Chains 25, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7257 restraints for refining 3023 atoms. 6622 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2226 (Rfree = 0.000) for 3023 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.2026 (Rfree = 0.000) for 3008 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 2995 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.1860 (Rfree = 0.000) for 2989 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.1796 (Rfree = 0.000) for 2979 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3076 seeds are put forward Round 1: 135 peptides, 26 chains. Longest chain 12 peptides. Score 0.313 Round 2: 157 peptides, 28 chains. Longest chain 13 peptides. Score 0.370 Round 3: 150 peptides, 23 chains. Longest chain 14 peptides. Score 0.429 Round 4: 153 peptides, 24 chains. Longest chain 14 peptides. Score 0.424 Round 5: 147 peptides, 21 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 5 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7523 restraints for refining 3024 atoms. 7040 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2055 (Rfree = 0.000) for 3024 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.1896 (Rfree = 0.000) for 3016 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.1795 (Rfree = 0.000) for 3008 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1753 (Rfree = 0.000) for 3000 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1814 (Rfree = 0.000) for 2993 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 3097 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3115 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.270 Round 2: 149 peptides, 27 chains. Longest chain 10 peptides. Score 0.355 Round 3: 157 peptides, 27 chains. Longest chain 14 peptides. Score 0.388 Round 4: 161 peptides, 28 chains. Longest chain 14 peptides. Score 0.386 Round 5: 155 peptides, 29 chains. Longest chain 14 peptides. Score 0.344 Taking the results from Round 3 Chains 27, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7425 restraints for refining 3023 atoms. 6932 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1912 (Rfree = 0.000) for 3023 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.1760 (Rfree = 0.000) for 3010 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.1711 (Rfree = 0.000) for 3001 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1729 (Rfree = 0.000) for 2994 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1636 (Rfree = 0.000) for 2985 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3085 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 9 peptides. Score 0.256 Round 2: 157 peptides, 25 chains. Longest chain 15 peptides. Score 0.422 Round 3: 144 peptides, 25 chains. Longest chain 12 peptides. Score 0.370 Round 4: 155 peptides, 27 chains. Longest chain 13 peptides. Score 0.380 Round 5: 160 peptides, 27 chains. Longest chain 18 peptides. Score 0.400 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 132, 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 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4300 reflections ( 99.54 % complete ) and 7379 restraints for refining 3024 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1847 (Rfree = 0.000) for 3024 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1758 (Rfree = 0.000) for 3010 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1610 (Rfree = 0.000) for 2998 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1614 (Rfree = 0.000) for 2990 atoms. Found 0 (16 requested) and removed 7 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:39:52 GMT 2018 Job finished. TimeTaking 32.67 Used memory is bytes: 22335064