Mon 24 Dec 08:05:25 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 2od6-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-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/2od6-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-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 08:05:30 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/2od6-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-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 300 and 0 Target number of residues in the AU: 300 Target solvent content: 0.6683 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-4.0-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: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.75 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: 29.066 4.001 Wilson plot Bfac: 90.57 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4445 reflections ( 98.32 % complete ) and 0 restraints for refining 3912 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3592 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3478 (Rfree = 0.000) for 3912 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 4001 seeds are put forward NCS extension: 0 residues added, 4001 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 8 peptides. Score 0.235 Round 2: 184 peptides, 34 chains. Longest chain 16 peptides. Score 0.349 Round 3: 191 peptides, 31 chains. Longest chain 15 peptides. Score 0.416 Round 4: 217 peptides, 36 chains. Longest chain 11 peptides. Score 0.430 Round 5: 206 peptides, 32 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 5 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 7584 restraints for refining 3179 atoms. 6920 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3141 (Rfree = 0.000) for 3179 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.3255 (Rfree = 0.000) for 3109 atoms. Found 7 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2854 (Rfree = 0.000) for 3060 atoms. Found 4 (14 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.3014 (Rfree = 0.000) for 3022 atoms. Found 8 (14 requested) and removed 17 (7 requested) atoms. Cycle 5: After refmac, R = 0.3046 (Rfree = 0.000) for 2985 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 3100 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3113 seeds are put forward Round 1: 141 peptides, 28 chains. Longest chain 9 peptides. Score 0.285 Round 2: 200 peptides, 36 chains. Longest chain 10 peptides. Score 0.374 Round 3: 208 peptides, 33 chains. Longest chain 11 peptides. Score 0.442 Round 4: 205 peptides, 33 chains. Longest chain 14 peptides. Score 0.433 Round 5: 200 peptides, 31 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 5 Chains 31, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 7098 restraints for refining 3053 atoms. 6453 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3143 (Rfree = 0.000) for 3053 atoms. Found 14 (14 requested) and removed 39 (7 requested) atoms. Cycle 7: After refmac, R = 0.2993 (Rfree = 0.000) for 2996 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 8: After refmac, R = 0.3031 (Rfree = 0.000) for 2955 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 9: After refmac, R = 0.2817 (Rfree = 0.000) for 2928 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2884 (Rfree = 0.000) for 2910 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 3027 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3050 seeds are put forward Round 1: 169 peptides, 34 chains. Longest chain 8 peptides. Score 0.295 Round 2: 196 peptides, 35 chains. Longest chain 13 peptides. Score 0.375 Round 3: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.404 Round 4: 188 peptides, 32 chains. Longest chain 11 peptides. Score 0.392 Round 5: 194 peptides, 34 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 3 Chains 30, Residues 153, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6513 restraints for refining 2918 atoms. 5874 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3066 (Rfree = 0.000) for 2918 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 12: After refmac, R = 0.3140 (Rfree = 0.000) for 2888 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 13: After refmac, R = 0.3063 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 14: After refmac, R = 0.2599 (Rfree = 0.000) for 2831 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.3088 (Rfree = 0.000) for 2811 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2934 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 8 peptides. Score 0.274 Round 2: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.368 Round 3: 192 peptides, 31 chains. Longest chain 12 peptides. Score 0.419 Round 4: 189 peptides, 29 chains. Longest chain 12 peptides. Score 0.438 Round 5: 197 peptides, 32 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Chains 29, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6943 restraints for refining 2973 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3163 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 34 (7 requested) atoms. Cycle 17: After refmac, R = 0.2991 (Rfree = 0.000) for 2919 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 18: After refmac, R = 0.2785 (Rfree = 0.000) for 2884 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 19: After refmac, R = 0.2706 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 20: After refmac, R = 0.2232 (Rfree = 0.000) for 2846 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2947 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 11 peptides. Score 0.279 Round 2: 175 peptides, 30 chains. Longest chain 13 peptides. Score 0.377 Round 3: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.399 Round 4: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.427 Round 5: 177 peptides, 27 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 5 Chains 27, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 7094 restraints for refining 3016 atoms. 6521 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2843 (Rfree = 0.000) for 3016 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 22: After refmac, R = 0.2839 (Rfree = 0.000) for 2975 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2843 (Rfree = 0.000) for 2946 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.2916 (Rfree = 0.000) for 2926 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 25: After refmac, R = 0.2919 (Rfree = 0.000) for 2903 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 3026 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3052 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 7 peptides. Score 0.258 Round 2: 145 peptides, 27 chains. Longest chain 9 peptides. Score 0.317 Round 3: 150 peptides, 26 chains. Longest chain 10 peptides. Score 0.351 Round 4: 171 peptides, 28 chains. Longest chain 15 peptides. Score 0.393 Round 5: 167 peptides, 27 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6548 restraints for refining 2925 atoms. 6015 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2969 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 27: After refmac, R = 0.2951 (Rfree = 0.000) for 2887 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 28: After refmac, R = 0.2691 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 29: After refmac, R = 0.2756 (Rfree = 0.000) for 2834 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 30: After refmac, R = 0.2656 (Rfree = 0.000) for 2809 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2934 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.237 Round 2: 157 peptides, 28 chains. Longest chain 19 peptides. Score 0.345 Round 3: 163 peptides, 28 chains. Longest chain 16 peptides. Score 0.366 Round 4: 163 peptides, 29 chains. Longest chain 16 peptides. Score 0.351 Round 5: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 5 Chains 28, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6412 restraints for refining 2884 atoms. 5892 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2827 (Rfree = 0.000) for 2884 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 32: After refmac, R = 0.2728 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 33: After refmac, R = 0.2867 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 34: After refmac, R = 0.2585 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 35: After refmac, R = 0.2771 (Rfree = 0.000) for 2786 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 2895 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2912 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 9 peptides. Score 0.244 Round 2: 158 peptides, 30 chains. Longest chain 11 peptides. Score 0.317 Round 3: 154 peptides, 27 chains. Longest chain 13 peptides. Score 0.349 Round 4: 165 peptides, 30 chains. Longest chain 9 peptides. Score 0.342 Round 5: 157 peptides, 27 chains. Longest chain 14 peptides. Score 0.360 Taking the results from Round 5 Chains 27, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6455 restraints for refining 2902 atoms. 5962 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3261 (Rfree = 0.000) for 2902 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 37: After refmac, R = 0.2899 (Rfree = 0.000) for 2867 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 38: After refmac, R = 0.2382 (Rfree = 0.000) for 2841 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 39: After refmac, R = 0.2857 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.2838 (Rfree = 0.000) for 2818 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2923 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 8 peptides. Score 0.245 Round 2: 163 peptides, 31 chains. Longest chain 12 peptides. Score 0.320 Round 3: 156 peptides, 27 chains. Longest chain 9 peptides. Score 0.357 Round 4: 148 peptides, 26 chains. Longest chain 10 peptides. Score 0.344 Round 5: 163 peptides, 27 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 5 Chains 27, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6307 restraints for refining 2882 atoms. 5790 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2837 (Rfree = 0.000) for 2882 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 42: After refmac, R = 0.2823 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 43: After refmac, R = 0.2627 (Rfree = 0.000) for 2830 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2760 (Rfree = 0.000) for 2821 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 45: After refmac, R = 0.2581 (Rfree = 0.000) for 2808 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2922 seeds are put forward Round 1: 106 peptides, 25 chains. Longest chain 6 peptides. Score 0.194 Round 2: 129 peptides, 27 chains. Longest chain 7 peptides. Score 0.255 Round 3: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.300 Round 4: 131 peptides, 25 chains. Longest chain 10 peptides. Score 0.296 Round 5: 130 peptides, 24 chains. Longest chain 11 peptides. Score 0.309 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 106, 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 2od6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4445 reflections ( 98.32 % complete ) and 6431 restraints for refining 2859 atoms. 6031 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2703 (Rfree = 0.000) for 2859 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2903 (Rfree = 0.000) for 2835 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2657 (Rfree = 0.000) for 2820 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2755 (Rfree = 0.000) for 2804 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 33.83