Mon 24 Dec 00:04:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-mrncs ############### 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 00:04:29 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-mrncs/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 314 and 0 Target number of residues in the AU: 314 Target solvent content: 0.6528 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: 2od6-3.6-parrot-mrncs.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: 2od6-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 79.53 Failed to save intermediate PDB 6060 reflections ( 98.76 % complete ) and 0 restraints for refining 3934 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3365 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3344 (Rfree = 0.000) for 3934 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 4026 seeds are put forward NCS extension: 0 residues added, 4026 seeds are put forward Round 1: 198 peptides, 38 chains. Longest chain 13 peptides. Score 0.338 Round 2: 252 peptides, 39 chains. Longest chain 13 peptides. Score 0.496 Round 3: 277 peptides, 35 chains. Longest chain 21 peptides. Score 0.608 Round 4: 276 peptides, 34 chains. Longest chain 20 peptides. Score 0.616 Round 5: 277 peptides, 34 chains. Longest chain 21 peptides. Score 0.619 Taking the results from Round 5 Chains 34, Residues 243, Estimated correctness of the model 21.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7113 restraints for refining 3190 atoms. 6175 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3250 (Rfree = 0.000) for 3190 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 2: After refmac, R = 0.3131 (Rfree = 0.000) for 3127 atoms. Found 12 (20 requested) and removed 24 (10 requested) atoms. Cycle 3: After refmac, R = 0.3123 (Rfree = 0.000) for 3071 atoms. Found 8 (19 requested) and removed 21 (9 requested) atoms. Cycle 4: After refmac, R = 0.3086 (Rfree = 0.000) for 3032 atoms. Found 12 (19 requested) and removed 21 (9 requested) atoms. Cycle 5: After refmac, R = 0.3153 (Rfree = 0.000) for 2992 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3093 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3124 seeds are put forward Round 1: 189 peptides, 36 chains. Longest chain 11 peptides. Score 0.337 Round 2: 236 peptides, 33 chains. Longest chain 18 peptides. Score 0.525 Round 3: 232 peptides, 34 chains. Longest chain 21 peptides. Score 0.501 Round 4: 230 peptides, 29 chains. Longest chain 20 peptides. Score 0.558 Round 5: 243 peptides, 37 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 4 Chains 29, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6896 restraints for refining 3071 atoms. 6121 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3034 (Rfree = 0.000) for 3071 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 7: After refmac, R = 0.2977 (Rfree = 0.000) for 3023 atoms. Found 18 (19 requested) and removed 25 (9 requested) atoms. Cycle 8: After refmac, R = 0.3108 (Rfree = 0.000) for 2995 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 9: After refmac, R = 0.2934 (Rfree = 0.000) for 2980 atoms. Found 16 (19 requested) and removed 22 (9 requested) atoms. Cycle 10: After refmac, R = 0.2973 (Rfree = 0.000) for 2964 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3126 seeds are put forward Round 1: 181 peptides, 35 chains. Longest chain 9 peptides. Score 0.323 Round 2: 203 peptides, 34 chains. Longest chain 13 peptides. Score 0.413 Round 3: 212 peptides, 31 chains. Longest chain 18 peptides. Score 0.482 Round 4: 219 peptides, 30 chains. Longest chain 18 peptides. Score 0.515 Round 5: 212 peptides, 34 chains. Longest chain 14 peptides. Score 0.441 Taking the results from Round 4 Chains 30, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6782 restraints for refining 3044 atoms. 6056 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3184 (Rfree = 0.000) for 3044 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 12: After refmac, R = 0.3074 (Rfree = 0.000) for 3011 atoms. Found 18 (19 requested) and removed 37 (9 requested) atoms. Cycle 13: After refmac, R = 0.2990 (Rfree = 0.000) for 2962 atoms. Found 10 (19 requested) and removed 20 (9 requested) atoms. Cycle 14: After refmac, R = 0.3058 (Rfree = 0.000) for 2926 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 15: After refmac, R = 0.2960 (Rfree = 0.000) for 2907 atoms. Found 6 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 3029 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3050 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 11 peptides. Score 0.297 Round 2: 192 peptides, 30 chains. Longest chain 15 peptides. Score 0.433 Round 3: 200 peptides, 32 chains. Longest chain 16 peptides. Score 0.431 Round 4: 207 peptides, 29 chains. Longest chain 14 peptides. Score 0.493 Round 5: 212 peptides, 29 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 5 Chains 29, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6694 restraints for refining 3052 atoms. 5991 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3076 (Rfree = 0.000) for 3052 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 17: After refmac, R = 0.3229 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 18: After refmac, R = 0.3008 (Rfree = 0.000) for 2986 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 19: After refmac, R = 0.2765 (Rfree = 0.000) for 2970 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 20: After refmac, R = 0.2712 (Rfree = 0.000) for 2960 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3084 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3101 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 9 peptides. Score 0.263 Round 2: 206 peptides, 39 chains. Longest chain 10 peptides. Score 0.351 Round 3: 215 peptides, 36 chains. Longest chain 15 peptides. Score 0.423 Round 4: 218 peptides, 34 chains. Longest chain 15 peptides. Score 0.460 Round 5: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Chains 34, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6726 restraints for refining 3082 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3068 (Rfree = 0.000) for 3082 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 22: After refmac, R = 0.2854 (Rfree = 0.000) for 3039 atoms. Found 13 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2840 (Rfree = 0.000) for 3007 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.2977 (Rfree = 0.000) for 2990 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.2754 (Rfree = 0.000) for 2978 atoms. Found 11 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3125 seeds are put forward Round 1: 145 peptides, 29 chains. Longest chain 10 peptides. Score 0.285 Round 2: 173 peptides, 32 chains. Longest chain 12 peptides. Score 0.340 Round 3: 185 peptides, 31 chains. Longest chain 15 peptides. Score 0.396 Round 4: 186 peptides, 29 chains. Longest chain 13 peptides. Score 0.428 Round 5: 189 peptides, 29 chains. Longest chain 19 peptides. Score 0.438 Taking the results from Round 5 Chains 29, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6799 restraints for refining 3025 atoms. 6188 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2971 (Rfree = 0.000) for 3025 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 27: After refmac, R = 0.2756 (Rfree = 0.000) for 2997 atoms. Found 17 (19 requested) and removed 22 (9 requested) atoms. Cycle 28: After refmac, R = 0.2395 (Rfree = 0.000) for 2971 atoms. Found 6 (19 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2628 (Rfree = 0.000) for 2955 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 30: After refmac, R = 0.3070 (Rfree = 0.000) for 2955 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3050 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3081 seeds are put forward Round 1: 169 peptides, 33 chains. Longest chain 9 peptides. Score 0.311 Round 2: 195 peptides, 33 chains. Longest chain 12 peptides. Score 0.401 Round 3: 204 peptides, 33 chains. Longest chain 19 peptides. Score 0.430 Round 4: 181 peptides, 30 chains. Longest chain 13 peptides. Score 0.397 Round 5: 184 peptides, 30 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 3 Chains 33, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6644 restraints for refining 3022 atoms. 5993 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2691 (Rfree = 0.000) for 3022 atoms. Found 9 (19 requested) and removed 25 (9 requested) atoms. Cycle 32: After refmac, R = 0.2488 (Rfree = 0.000) for 2989 atoms. Found 13 (19 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2528 (Rfree = 0.000) for 2973 atoms. Found 4 (19 requested) and removed 19 (9 requested) atoms. Cycle 34: After refmac, R = 0.2528 (Rfree = 0.000) for 2947 atoms. Found 13 (18 requested) and removed 18 (9 requested) atoms. Cycle 35: After refmac, R = 0.2619 (Rfree = 0.000) for 2929 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3029 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 10 peptides. Score 0.281 Round 2: 176 peptides, 33 chains. Longest chain 10 peptides. Score 0.336 Round 3: 174 peptides, 31 chains. Longest chain 14 peptides. Score 0.359 Round 4: 186 peptides, 32 chains. Longest chain 13 peptides. Score 0.385 Round 5: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.370 Taking the results from Round 4 Chains 32, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6697 restraints for refining 3019 atoms. 6113 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2965 (Rfree = 0.000) for 3019 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 37: After refmac, R = 0.2763 (Rfree = 0.000) for 2988 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 38: After refmac, R = 0.2774 (Rfree = 0.000) for 2967 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.2883 (Rfree = 0.000) for 2963 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.2676 (Rfree = 0.000) for 2957 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3052 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3071 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 6 peptides. Score 0.229 Round 2: 156 peptides, 29 chains. Longest chain 8 peptides. Score 0.325 Round 3: 159 peptides, 29 chains. Longest chain 12 peptides. Score 0.336 Round 4: 155 peptides, 27 chains. Longest chain 12 peptides. Score 0.353 Round 5: 167 peptides, 29 chains. Longest chain 13 peptides. Score 0.365 Taking the results from Round 5 Chains 29, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6620 restraints for refining 2950 atoms. 6097 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3060 (Rfree = 0.000) for 2950 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 42: After refmac, R = 0.2671 (Rfree = 0.000) for 2930 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.2710 (Rfree = 0.000) for 2916 atoms. Found 17 (18 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.2957 (Rfree = 0.000) for 2902 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.2548 (Rfree = 0.000) for 2898 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 2975 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 7 peptides. Score 0.207 Round 2: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.303 Round 3: 132 peptides, 26 chains. Longest chain 7 peptides. Score 0.284 Round 4: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.313 Round 5: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, 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 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6060 reflections ( 98.76 % complete ) and 6277 restraints for refining 2852 atoms. 5879 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2832 (Rfree = 0.000) for 2852 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2583 (Rfree = 0.000) for 2838 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2545 (Rfree = 0.000) for 2823 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2573 (Rfree = 0.000) for 2811 atoms. TimeTaking 39.62