Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-hancs/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-hancs.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-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.80 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 3916 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3554 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3389 (Rfree = 0.000) for 3916 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 4008 seeds are put forward NCS extension: 0 residues added, 4008 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 9 peptides. Score 0.282 Round 2: 209 peptides, 34 chains. Longest chain 14 peptides. Score 0.432 Round 3: 208 peptides, 29 chains. Longest chain 19 peptides. Score 0.496 Round 4: 217 peptides, 28 chains. Longest chain 14 peptides. Score 0.535 Round 5: 225 peptides, 30 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 4 Chains 28, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 7473 restraints for refining 3178 atoms. 6745 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3064 (Rfree = 0.000) for 3178 atoms. Found 8 (15 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.3029 (Rfree = 0.000) for 3099 atoms. Found 8 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2659 (Rfree = 0.000) for 3037 atoms. Found 3 (14 requested) and removed 20 (7 requested) atoms. Cycle 4: After refmac, R = 0.2988 (Rfree = 0.000) for 2994 atoms. Found 4 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2704 (Rfree = 0.000) for 2957 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3104 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 13 peptides. Score 0.281 Round 2: 196 peptides, 35 chains. Longest chain 11 peptides. Score 0.375 Round 3: 210 peptides, 33 chains. Longest chain 19 peptides. Score 0.449 Round 4: 200 peptides, 31 chains. Longest chain 20 peptides. Score 0.445 Round 5: 213 peptides, 32 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 32, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6958 restraints for refining 3014 atoms. 6266 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3020 (Rfree = 0.000) for 3014 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 7: After refmac, R = 0.2894 (Rfree = 0.000) for 2955 atoms. Found 13 (14 requested) and removed 19 (7 requested) atoms. Cycle 8: After refmac, R = 0.2938 (Rfree = 0.000) for 2931 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.2392 (Rfree = 0.000) for 2910 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2805 (Rfree = 0.000) for 2892 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 3015 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3040 seeds are put forward Round 1: 157 peptides, 33 chains. Longest chain 7 peptides. Score 0.266 Round 2: 178 peptides, 33 chains. Longest chain 9 peptides. Score 0.343 Round 3: 205 peptides, 35 chains. Longest chain 12 peptides. Score 0.405 Round 4: 193 peptides, 30 chains. Longest chain 13 peptides. Score 0.437 Round 5: 193 peptides, 31 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 4 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6450 restraints for refining 2894 atoms. 5828 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3170 (Rfree = 0.000) for 2894 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 12: After refmac, R = 0.3021 (Rfree = 0.000) for 2853 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 13: After refmac, R = 0.2552 (Rfree = 0.000) for 2830 atoms. Found 7 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.2574 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2962 (Rfree = 0.000) for 2793 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2911 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 9 peptides. Score 0.275 Round 2: 179 peptides, 31 chains. Longest chain 15 peptides. Score 0.376 Round 3: 188 peptides, 33 chains. Longest chain 12 peptides. Score 0.377 Round 4: 196 peptides, 32 chains. Longest chain 18 peptides. Score 0.418 Round 5: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.410 Taking the results from Round 4 Chains 32, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6288 restraints for refining 2841 atoms. 5664 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3063 (Rfree = 0.000) for 2841 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 17: After refmac, R = 0.3062 (Rfree = 0.000) for 2812 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 18: After refmac, R = 0.2823 (Rfree = 0.000) for 2789 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.2586 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2926 (Rfree = 0.000) for 2769 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.75 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 2904 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 8 peptides. Score 0.246 Round 2: 165 peptides, 30 chains. Longest chain 10 peptides. Score 0.342 Round 3: 178 peptides, 32 chains. Longest chain 10 peptides. Score 0.358 Round 4: 171 peptides, 27 chains. Longest chain 15 peptides. Score 0.408 Round 5: 164 peptides, 29 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 4 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6355 restraints for refining 2811 atoms. 5806 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3242 (Rfree = 0.000) for 2811 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.3083 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.2870 (Rfree = 0.000) for 2731 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2956 (Rfree = 0.000) for 2725 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.2903 (Rfree = 0.000) for 2711 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.72 Search for helices and strands: 0 residues in 0 chains, 2776 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2794 seeds are put forward Round 1: 145 peptides, 32 chains. Longest chain 8 peptides. Score 0.236 Round 2: 158 peptides, 32 chains. Longest chain 9 peptides. Score 0.286 Round 3: 171 peptides, 32 chains. Longest chain 10 peptides. Score 0.333 Round 4: 168 peptides, 30 chains. Longest chain 16 peptides. Score 0.353 Round 5: 165 peptides, 32 chains. Longest chain 14 peptides. Score 0.311 Taking the results from Round 4 Chains 30, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6503 restraints for refining 2828 atoms. 5981 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3061 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 27: After refmac, R = 0.3027 (Rfree = 0.000) for 2786 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.3109 (Rfree = 0.000) for 2761 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 29: After refmac, R = 0.2934 (Rfree = 0.000) for 2738 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 30: After refmac, R = 0.3006 (Rfree = 0.000) for 2718 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 2799 seeds are put forward NCS extension: 0 residues added, 2799 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 8 peptides. Score 0.217 Round 2: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.261 Round 3: 148 peptides, 30 chains. Longest chain 9 peptides. Score 0.280 Round 4: 153 peptides, 28 chains. Longest chain 9 peptides. Score 0.330 Round 5: 154 peptides, 29 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 4 Chains 28, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6220 restraints for refining 2740 atoms. 5748 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3114 (Rfree = 0.000) for 2740 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 32: After refmac, R = 0.2977 (Rfree = 0.000) for 2703 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.3027 (Rfree = 0.000) for 2684 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.2506 (Rfree = 0.000) for 2665 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2531 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 2740 seeds are put forward NCS extension: 0 residues added, 2740 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.261 Round 2: 135 peptides, 28 chains. Longest chain 7 peptides. Score 0.262 Round 3: 132 peptides, 25 chains. Longest chain 8 peptides. Score 0.300 Round 4: 145 peptides, 30 chains. Longest chain 7 peptides. Score 0.268 Round 5: 140 peptides, 25 chains. Longest chain 10 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 ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6062 restraints for refining 2675 atoms. 5627 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2854 (Rfree = 0.000) for 2675 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.2859 (Rfree = 0.000) for 2650 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.2796 (Rfree = 0.000) for 2638 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2327 (Rfree = 0.000) for 2627 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.2237 (Rfree = 0.000) for 2619 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 2682 seeds are put forward NCS extension: 0 residues added, 2682 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 6 peptides. Score 0.220 Round 2: 130 peptides, 29 chains. Longest chain 7 peptides. Score 0.226 Round 3: 131 peptides, 26 chains. Longest chain 10 peptides. Score 0.280 Round 4: 130 peptides, 25 chains. Longest chain 10 peptides. Score 0.293 Round 5: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.301 Taking the results from Round 5 Chains 24, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6212 restraints for refining 2717 atoms. 5820 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2973 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 42: After refmac, R = 0.2810 (Rfree = 0.000) for 2697 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 43: After refmac, R = 0.2914 (Rfree = 0.000) for 2688 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 44: After refmac, R = 0.2751 (Rfree = 0.000) for 2679 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2869 (Rfree = 0.000) for 2674 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 2752 seeds are put forward NCS extension: 0 residues added, 2752 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 8 peptides. Score 0.213 Round 2: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.281 Round 3: 99 peptides, 21 chains. Longest chain 9 peptides. Score 0.236 Round 4: 107 peptides, 20 chains. Longest chain 12 peptides. Score 0.287 Round 5: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.273 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 87, 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 5695 restraints for refining 2592 atoms. 5367 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3038 (Rfree = 0.000) for 2592 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2794 (Rfree = 0.000) for 2567 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2398 (Rfree = 0.000) for 2549 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2251 (Rfree = 0.000) for 2530 atoms. TimeTaking 48.95