Mon 24 Dec 07:29:23 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 2od6-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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/2od6-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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 07:29:28 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/2od6-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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 304 and 0 Target number of residues in the AU: 304 Target solvent content: 0.6639 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: 2od6-3.8-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: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 3.800 Wilson plot Bfac: 87.53 5189 reflections ( 98.56 % complete ) and 0 restraints for refining 3882 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3555 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3537 (Rfree = 0.000) for 3882 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 3955 seeds are put forward NCS extension: 0 residues added, 3955 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 11 peptides. Score 0.254 Round 2: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.353 Round 3: 205 peptides, 35 chains. Longest chain 13 peptides. Score 0.405 Round 4: 225 peptides, 39 chains. Longest chain 16 peptides. Score 0.414 Round 5: 227 peptides, 36 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 5 Chains 36, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7452 restraints for refining 3182 atoms. 6724 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3173 (Rfree = 0.000) for 3182 atoms. Found 13 (17 requested) and removed 22 (8 requested) atoms. Cycle 2: After refmac, R = 0.2991 (Rfree = 0.000) for 3108 atoms. Found 12 (17 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2910 (Rfree = 0.000) for 3063 atoms. Found 11 (17 requested) and removed 15 (8 requested) atoms. Cycle 4: After refmac, R = 0.3014 (Rfree = 0.000) for 3029 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2895 (Rfree = 0.000) for 3006 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 3122 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3140 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 7 peptides. Score 0.234 Round 2: 179 peptides, 33 chains. Longest chain 9 peptides. Score 0.346 Round 3: 193 peptides, 32 chains. Longest chain 11 peptides. Score 0.408 Round 4: 203 peptides, 34 chains. Longest chain 12 peptides. Score 0.413 Round 5: 200 peptides, 31 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 5 Chains 31, Residues 169, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6964 restraints for refining 3060 atoms. 6273 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2952 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 7: After refmac, R = 0.2883 (Rfree = 0.000) for 3016 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2716 (Rfree = 0.000) for 2987 atoms. Found 11 (16 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.2403 (Rfree = 0.000) for 2969 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2677 (Rfree = 0.000) for 2954 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3071 seeds are put forward Round 1: 174 peptides, 33 chains. Longest chain 10 peptides. Score 0.329 Round 2: 227 peptides, 38 chains. Longest chain 17 peptides. Score 0.434 Round 3: 204 peptides, 35 chains. Longest chain 13 peptides. Score 0.402 Round 4: 203 peptides, 32 chains. Longest chain 11 peptides. Score 0.440 Round 5: 196 peptides, 33 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 32, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6965 restraints for refining 3080 atoms. 6313 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2972 (Rfree = 0.000) for 3080 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2758 (Rfree = 0.000) for 3037 atoms. Found 12 (16 requested) and removed 24 (8 requested) atoms. Cycle 13: After refmac, R = 0.3045 (Rfree = 0.000) for 2999 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 14: After refmac, R = 0.2814 (Rfree = 0.000) for 2975 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.2858 (Rfree = 0.000) for 2958 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 3076 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3082 seeds are put forward Round 1: 160 peptides, 35 chains. Longest chain 9 peptides. Score 0.246 Round 2: 180 peptides, 33 chains. Longest chain 10 peptides. Score 0.350 Round 3: 185 peptides, 33 chains. Longest chain 10 peptides. Score 0.367 Round 4: 201 peptides, 32 chains. Longest chain 21 peptides. Score 0.434 Round 5: 191 peptides, 34 chains. Longest chain 9 peptides. Score 0.373 Taking the results from Round 4 Chains 32, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6604 restraints for refining 2991 atoms. 5960 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3027 (Rfree = 0.000) for 2991 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 17: After refmac, R = 0.2802 (Rfree = 0.000) for 2956 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2735 (Rfree = 0.000) for 2938 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.2664 (Rfree = 0.000) for 2915 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2499 (Rfree = 0.000) for 2900 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 3004 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3029 seeds are put forward Round 1: 142 peptides, 29 chains. Longest chain 9 peptides. Score 0.273 Round 2: 186 peptides, 35 chains. Longest chain 11 peptides. Score 0.341 Round 3: 185 peptides, 35 chains. Longest chain 9 peptides. Score 0.337 Round 4: 183 peptides, 32 chains. Longest chain 10 peptides. Score 0.375 Round 5: 185 peptides, 31 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 5 Chains 31, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5189 reflections ( 98.56 % complete ) and 6979 restraints for refining 3045 atoms. 6394 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2983 (Rfree = 0.000) for 3045 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 22: After refmac, R = 0.2730 (Rfree = 0.000) for 3005 atoms. Found 12 (16 requested) and removed 26 (8 requested) atoms. Cycle 23: After refmac, R = 0.2843 (Rfree = 0.000) for 2972 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.2609 (Rfree = 0.000) for 2958 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.2869 (Rfree = 0.000) for 2946 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 3034 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3047 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.261 Round 2: 181 peptides, 32 chains. Longest chain 10 peptides. Score 0.368 Round 3: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.390 Round 4: 183 peptides, 27 chains. Longest chain 12 peptides. Score 0.447 Round 5: 186 peptides, 30 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Chains 27, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6591 restraints for refining 2960 atoms. 5994 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3050 (Rfree = 0.000) for 2960 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 27: After refmac, R = 0.2893 (Rfree = 0.000) for 2934 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2715 (Rfree = 0.000) for 2911 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.2883 (Rfree = 0.000) for 2902 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.2254 (Rfree = 0.000) for 2883 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 2977 seeds are put forward NCS extension: 0 residues added, 2977 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 8 peptides. Score 0.232 Round 2: 158 peptides, 28 chains. Longest chain 13 peptides. Score 0.348 Round 3: 156 peptides, 27 chains. Longest chain 14 peptides. Score 0.357 Round 4: 165 peptides, 30 chains. Longest chain 9 peptides. Score 0.342 Round 5: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.354 Taking the results from Round 3 Chains 27, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6230 restraints for refining 2801 atoms. 5741 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3057 (Rfree = 0.000) for 2801 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.2717 (Rfree = 0.000) for 2783 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2808 (Rfree = 0.000) for 2779 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.2684 (Rfree = 0.000) for 2771 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.2609 (Rfree = 0.000) for 2759 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 2872 seeds are put forward NCS extension: 0 residues added, 2872 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 7 peptides. Score 0.221 Round 2: 151 peptides, 30 chains. Longest chain 8 peptides. Score 0.291 Round 3: 145 peptides, 29 chains. Longest chain 8 peptides. Score 0.285 Round 4: 143 peptides, 26 chains. Longest chain 9 peptides. Score 0.325 Round 5: 140 peptides, 25 chains. Longest chain 8 peptides. Score 0.330 Taking the results from Round 5 Chains 25, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6194 restraints for refining 2823 atoms. 5759 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2918 (Rfree = 0.000) for 2823 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 37: After refmac, R = 0.2804 (Rfree = 0.000) for 2795 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 38: After refmac, R = 0.2886 (Rfree = 0.000) for 2782 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.2447 (Rfree = 0.000) for 2767 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 40: After refmac, R = 0.2686 (Rfree = 0.000) for 2759 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward NCS extension: 0 residues added, 2866 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 8 peptides. Score 0.220 Round 2: 150 peptides, 31 chains. Longest chain 8 peptides. Score 0.271 Round 3: 141 peptides, 25 chains. Longest chain 11 peptides. Score 0.334 Round 4: 143 peptides, 27 chains. Longest chain 12 peptides. Score 0.309 Round 5: 134 peptides, 25 chains. Longest chain 8 peptides. Score 0.308 Taking the results from Round 3 Chains 25, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6070 restraints for refining 2769 atoms. 5631 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2819 (Rfree = 0.000) for 2769 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 42: After refmac, R = 0.2777 (Rfree = 0.000) for 2753 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.2292 (Rfree = 0.000) for 2743 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2187 (Rfree = 0.000) for 2731 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2144 (Rfree = 0.000) for 2719 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 0 residues added, 2786 seeds are put forward Round 1: 144 peptides, 32 chains. Longest chain 8 peptides. Score 0.232 Round 2: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.278 Round 3: 170 peptides, 33 chains. Longest chain 9 peptides. Score 0.314 Round 4: 155 peptides, 29 chains. Longest chain 8 peptides. Score 0.322 Round 5: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.345 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 139, 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 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5189 reflections ( 98.56 % complete ) and 6270 restraints for refining 2846 atoms. 5745 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2830 (Rfree = 0.000) for 2846 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2843 (Rfree = 0.000) for 2820 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2660 (Rfree = 0.000) for 2805 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2282 (Rfree = 0.000) for 2787 atoms. TimeTaking 34.55