null Mon 24 Dec 07:32:24 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 2itb-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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/2itb-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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 07:32:29 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/2itb-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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 241 and 0 Target number of residues in the AU: 241 Target solvent content: 0.6396 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-3.4-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: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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: 53.913 3.401 Wilson plot Bfac: 71.79 5306 reflections ( 99.72 % complete ) and 0 restraints for refining 3645 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3665 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3083 (Rfree = 0.000) for 3645 atoms. Found 7 (27 requested) and removed 43 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 0 residues added, 3702 seeds are put forward Round 1: 103 peptides, 24 chains. Longest chain 7 peptides. Score 0.206 Round 2: 134 peptides, 29 chains. Longest chain 8 peptides. Score 0.260 Round 3: 155 peptides, 31 chains. Longest chain 9 peptides. Score 0.321 Round 4: 158 peptides, 31 chains. Longest chain 10 peptides. Score 0.335 Round 5: 162 peptides, 33 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 4 Chains 31, Residues 127, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7198 restraints for refining 2995 atoms. 6710 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2950 (Rfree = 0.000) for 2995 atoms. Found 11 (22 requested) and removed 21 (11 requested) atoms. Cycle 2: After refmac, R = 0.2793 (Rfree = 0.000) for 2969 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. Cycle 3: After refmac, R = 0.2820 (Rfree = 0.000) for 2955 atoms. Found 1 (22 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2746 (Rfree = 0.000) for 2940 atoms. Found 2 (22 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2724 (Rfree = 0.000) for 2928 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 3053 seeds are put forward NCS extension: 0 residues added, 3053 seeds are put forward Round 1: 144 peptides, 33 chains. Longest chain 7 peptides. Score 0.228 Round 2: 164 peptides, 30 chains. Longest chain 9 peptides. Score 0.382 Round 3: 166 peptides, 31 chains. Longest chain 12 peptides. Score 0.372 Round 4: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.390 Round 5: 181 peptides, 33 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 5 Chains 33, Residues 148, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6737 restraints for refining 2871 atoms. 6167 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3067 (Rfree = 0.000) for 2871 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 7: After refmac, R = 0.2874 (Rfree = 0.000) for 2871 atoms. Found 3 (21 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.2930 (Rfree = 0.000) for 2854 atoms. Found 4 (21 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.2846 (Rfree = 0.000) for 2842 atoms. Found 0 (21 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2771 (Rfree = 0.000) for 2829 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2992 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 8 peptides. Score 0.286 Round 2: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.373 Round 3: 169 peptides, 30 chains. Longest chain 15 peptides. Score 0.404 Round 4: 162 peptides, 24 chains. Longest chain 13 peptides. Score 0.483 Round 5: 165 peptides, 26 chains. Longest chain 15 peptides. Score 0.460 Taking the results from Round 4 Chains 24, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6810 restraints for refining 2856 atoms. 6282 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3097 (Rfree = 0.000) for 2856 atoms. Found 15 (21 requested) and removed 14 (10 requested) atoms. Cycle 12: After refmac, R = 0.2970 (Rfree = 0.000) for 2854 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 13: After refmac, R = 0.2918 (Rfree = 0.000) for 2844 atoms. Found 1 (21 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.2886 (Rfree = 0.000) for 2832 atoms. Found 2 (21 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.2843 (Rfree = 0.000) for 2823 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 0 residues added, 2958 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 8 peptides. Score 0.266 Round 2: 159 peptides, 31 chains. Longest chain 12 peptides. Score 0.340 Round 3: 164 peptides, 28 chains. Longest chain 13 peptides. Score 0.419 Round 4: 165 peptides, 26 chains. Longest chain 12 peptides. Score 0.460 Round 5: 176 peptides, 25 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 5 Chains 26, Residues 151, Estimated correctness of the model 0.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6590 restraints for refining 2873 atoms. 5982 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3198 (Rfree = 0.000) for 2873 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 17: After refmac, R = 0.3075 (Rfree = 0.000) for 2867 atoms. Found 5 (21 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.3081 (Rfree = 0.000) for 2852 atoms. Found 5 (21 requested) and removed 17 (10 requested) atoms. Cycle 19: After refmac, R = 0.3040 (Rfree = 0.000) for 2836 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.3003 (Rfree = 0.000) for 2829 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 2960 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2979 seeds are put forward Round 1: 133 peptides, 29 chains. Longest chain 7 peptides. Score 0.255 Round 2: 158 peptides, 30 chains. Longest chain 10 peptides. Score 0.355 Round 3: 161 peptides, 29 chains. Longest chain 17 peptides. Score 0.387 Round 4: 161 peptides, 29 chains. Longest chain 18 peptides. Score 0.387 Round 5: 177 peptides, 31 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 31, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6740 restraints for refining 2882 atoms. 6187 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3171 (Rfree = 0.000) for 2882 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 22: After refmac, R = 0.3032 (Rfree = 0.000) for 2877 atoms. Found 0 (21 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.2981 (Rfree = 0.000) for 2862 atoms. Found 1 (21 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.2946 (Rfree = 0.000) for 2844 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.2913 (Rfree = 0.000) for 2835 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2961 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2987 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 11 peptides. Score 0.269 Round 2: 147 peptides, 26 chains. Longest chain 20 peptides. Score 0.382 Round 3: 158 peptides, 30 chains. Longest chain 16 peptides. Score 0.355 Round 4: 148 peptides, 24 chains. Longest chain 16 peptides. Score 0.425 Round 5: 148 peptides, 25 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 4 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6757 restraints for refining 2910 atoms. 6212 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3128 (Rfree = 0.000) for 2910 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.3011 (Rfree = 0.000) for 2907 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.2958 (Rfree = 0.000) for 2897 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2927 (Rfree = 0.000) for 2888 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2903 (Rfree = 0.000) for 2880 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 3015 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3038 seeds are put forward Round 1: 125 peptides, 28 chains. Longest chain 7 peptides. Score 0.235 Round 2: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.318 Round 3: 135 peptides, 28 chains. Longest chain 10 peptides. Score 0.286 Round 4: 133 peptides, 26 chains. Longest chain 8 peptides. Score 0.317 Round 5: 128 peptides, 26 chains. Longest chain 10 peptides. Score 0.292 Taking the results from Round 2 Chains 25, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7217 restraints for refining 2909 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3049 (Rfree = 0.000) for 2909 atoms. Found 11 (21 requested) and removed 11 (10 requested) atoms. Cycle 32: After refmac, R = 0.2956 (Rfree = 0.000) for 2908 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.2945 (Rfree = 0.000) for 2899 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2883 (Rfree = 0.000) for 2891 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2843 (Rfree = 0.000) for 2882 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 2999 seeds are put forward NCS extension: 0 residues added, 2999 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 7 peptides. Score 0.242 Round 2: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.297 Round 3: 134 peptides, 26 chains. Longest chain 10 peptides. Score 0.321 Round 4: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.355 Round 5: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 5 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7122 restraints for refining 2898 atoms. 6711 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3118 (Rfree = 0.000) for 2898 atoms. Found 16 (21 requested) and removed 10 (10 requested) atoms. Cycle 37: After refmac, R = 0.2981 (Rfree = 0.000) for 2904 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.2948 (Rfree = 0.000) for 2896 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2912 (Rfree = 0.000) for 2887 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2897 (Rfree = 0.000) for 2877 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2975 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.210 Round 2: 105 peptides, 21 chains. Longest chain 7 peptides. Score 0.283 Round 3: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.292 Round 4: 119 peptides, 24 chains. Longest chain 11 peptides. Score 0.289 Round 5: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.299 Taking the results from Round 5 Chains 24, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7101 restraints for refining 2878 atoms. 6737 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3102 (Rfree = 0.000) for 2878 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.3027 (Rfree = 0.000) for 2877 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2977 (Rfree = 0.000) for 2868 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2945 (Rfree = 0.000) for 2860 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2957 (Rfree = 0.000) for 2850 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 2990 seeds are put forward NCS extension: 0 residues added, 2990 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 10 peptides. Score 0.248 Round 2: 129 peptides, 24 chains. Longest chain 11 peptides. Score 0.338 Round 3: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.336 Round 4: 129 peptides, 25 chains. Longest chain 12 peptides. Score 0.318 Round 5: 128 peptides, 24 chains. Longest chain 10 peptides. Score 0.333 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 105, 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 2itb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5306 reflections ( 99.72 % complete ) and 6989 restraints for refining 2844 atoms. 6593 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3048 (Rfree = 0.000) for 2844 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. Cycle 47: After refmac, R = 0.3016 (Rfree = 0.000) for 2841 atoms. Found 0 (21 requested) and removed 2 (10 requested) atoms. Cycle 48: After refmac, R = 0.3000 (Rfree = 0.000) for 2839 atoms. Found 0 (21 requested) and removed 0 (10 requested) atoms. Cycle 49: After refmac, R = 0.2984 (Rfree = 0.000) for 2839 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:03:24 GMT 2018 Job finished. TimeTaking 31 Used memory is bytes: 1577032