Mon 24 Dec 07:26:56 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 2ooj-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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/2ooj-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 07:27:01 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/2ooj-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-4.0-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6382 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-4.0-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: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.65 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: 53.043 4.000 Wilson plot Bfac: 70.85 2539 reflections ( 98.68 % complete ) and 0 restraints for refining 2495 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3737 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3080 (Rfree = 0.000) for 2495 atoms. Found 8 (11 requested) and removed 29 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 2485 seeds are put forward NCS extension: 0 residues added, 2485 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.213 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.348 Round 3: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.367 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.399 Round 5: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 4 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5276 restraints for refining 2037 atoms. 4975 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2890 (Rfree = 0.000) for 2037 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 2: After refmac, R = 0.2737 (Rfree = 0.000) for 2018 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2694 (Rfree = 0.000) for 2011 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2617 (Rfree = 0.000) for 2001 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 5: After refmac, R = 0.2773 (Rfree = 0.000) for 1999 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward NCS extension: 0 residues added, 2014 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.306 Round 2: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.358 Round 3: 99 peptides, 17 chains. Longest chain 13 peptides. Score 0.377 Round 4: 98 peptides, 16 chains. Longest chain 12 peptides. Score 0.397 Round 5: 94 peptides, 15 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5111 restraints for refining 1992 atoms. 4810 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3034 (Rfree = 0.000) for 1992 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.3137 (Rfree = 0.000) for 1991 atoms. Found 1 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.3060 (Rfree = 0.000) for 1981 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.3067 (Rfree = 0.000) for 1974 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2960 (Rfree = 0.000) for 1963 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 1977 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1980 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 10 peptides. Score 0.254 Round 2: 90 peptides, 15 chains. Longest chain 12 peptides. Score 0.375 Round 3: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.399 Round 4: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.363 Round 5: 94 peptides, 18 chains. Longest chain 10 peptides. Score 0.319 Taking the results from Round 3 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4909 restraints for refining 1953 atoms. 4608 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3015 (Rfree = 0.000) for 1953 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.3190 (Rfree = 0.000) for 1947 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.3084 (Rfree = 0.000) for 1940 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.3111 (Rfree = 0.000) for 1935 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.3023 (Rfree = 0.000) for 1930 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 1964 seeds are put forward NCS extension: 0 residues added, 1964 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 10 peptides. Score 0.238 Round 2: 89 peptides, 15 chains. Longest chain 12 peptides. Score 0.369 Round 3: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.391 Round 4: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.403 Round 5: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.441 Taking the results from Round 5 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4976 restraints for refining 1988 atoms. 4621 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3099 (Rfree = 0.000) for 1988 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2880 (Rfree = 0.000) for 1985 atoms. Found 2 (9 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2801 (Rfree = 0.000) for 1973 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2827 (Rfree = 0.000) for 1966 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2799 (Rfree = 0.000) for 1959 atoms. Found 3 (9 requested) and removed 35 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 1944 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1960 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 10 peptides. Score 0.226 Round 2: 92 peptides, 19 chains. Longest chain 12 peptides. Score 0.278 Round 3: 89 peptides, 19 chains. Longest chain 8 peptides. Score 0.258 Round 4: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.280 Round 5: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 5 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5244 restraints for refining 2037 atoms. 4941 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3186 (Rfree = 0.000) for 2037 atoms. Found 6 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.3022 (Rfree = 0.000) for 2024 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.3223 (Rfree = 0.000) for 2020 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2911 (Rfree = 0.000) for 2014 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.3136 (Rfree = 0.000) for 2010 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 0 residues added, 2048 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 6 peptides. Score 0.203 Round 2: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.342 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 5: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 3 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 4961 restraints for refining 2037 atoms. 4613 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3107 (Rfree = 0.000) for 2037 atoms. Found 8 (9 requested) and removed 70 (4 requested) atoms. Cycle 27: After refmac, R = 0.2947 (Rfree = 0.000) for 1973 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2937 (Rfree = 0.000) for 1970 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2823 (Rfree = 0.000) for 1966 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2784 (Rfree = 0.000) for 1960 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.86 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 0 residues added, 1996 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 2: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.323 Round 3: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.302 Round 4: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.365 Round 5: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5199 restraints for refining 2018 atoms. 4933 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3015 (Rfree = 0.000) for 2018 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2910 (Rfree = 0.000) for 2016 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2691 (Rfree = 0.000) for 2012 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2785 (Rfree = 0.000) for 2007 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2855 (Rfree = 0.000) for 2003 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 0 residues added, 2030 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.251 Round 2: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.312 Round 3: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.293 Round 4: 70 peptides, 12 chains. Longest chain 8 peptides. Score 0.332 Round 5: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5280 restraints for refining 2037 atoms. 5035 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2695 (Rfree = 0.000) for 2037 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2594 (Rfree = 0.000) for 2034 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2550 (Rfree = 0.000) for 2029 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2520 (Rfree = 0.000) for 2025 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2497 (Rfree = 0.000) for 2023 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.247 Round 2: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.342 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.318 Round 4: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.348 Round 5: 94 peptides, 17 chains. Longest chain 8 peptides. Score 0.346 Taking the results from Round 4 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2539 reflections ( 98.68 % complete ) and 5244 restraints for refining 2037 atoms. 4964 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2847 (Rfree = 0.000) for 2037 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2812 (Rfree = 0.000) for 2033 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.3003 (Rfree = 0.000) for 2029 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2486 (Rfree = 0.000) for 2028 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.3060 (Rfree = 0.000) for 2024 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 0 residues added, 2052 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.274 Round 2: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.277 Round 3: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.309 Round 4: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.335 Round 5: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 59, 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 2ooj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2539 reflections ( 98.68 % complete ) and 5313 restraints for refining 2035 atoms. 5089 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3204 (Rfree = 0.000) for 2035 atoms. Found 0 (9 requested) and removed 1 (4 requested) atoms. Cycle 47: After refmac, R = 0.2675 (Rfree = 0.000) for 2033 atoms. Found 0 (9 requested) and removed 1 (4 requested) atoms. Cycle 48: After refmac, R = 0.2555 (Rfree = 0.000) for 2032 atoms. Found 0 (9 requested) and removed 0 (4 requested) atoms. Cycle 49: After refmac, R = 0.2535 (Rfree = 0.000) for 2032 atoms. TimeTaking 28.53