Mon 24 Dec 08:07:45 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 2od6-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-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/2od6-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-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 08:07:50 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/2od6-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-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 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-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: 2od6-3.6-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 3.600 Wilson plot Bfac: 79.53 6060 reflections ( 98.76 % complete ) and 0 restraints for refining 3875 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3474 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3597 (Rfree = 0.000) for 3875 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3964 seeds are put forward NCS extension: 0 residues added, 3964 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 11 peptides. Score 0.287 Round 2: 226 peptides, 37 chains. Longest chain 14 peptides. Score 0.444 Round 3: 247 peptides, 38 chains. Longest chain 15 peptides. Score 0.494 Round 4: 238 peptides, 32 chains. Longest chain 21 peptides. Score 0.543 Round 5: 246 peptides, 30 chains. Longest chain 19 peptides. Score 0.588 Taking the results from Round 5 Chains 30, Residues 216, Estimated correctness of the model 9.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7282 restraints for refining 3190 atoms. 6448 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3259 (Rfree = 0.000) for 3190 atoms. Found 10 (20 requested) and removed 24 (10 requested) atoms. Cycle 2: After refmac, R = 0.3264 (Rfree = 0.000) for 3119 atoms. Found 13 (20 requested) and removed 24 (10 requested) atoms. Cycle 3: After refmac, R = 0.3071 (Rfree = 0.000) for 3063 atoms. Found 9 (19 requested) and removed 18 (9 requested) atoms. Cycle 4: After refmac, R = 0.3107 (Rfree = 0.000) for 3031 atoms. Found 11 (19 requested) and removed 21 (9 requested) atoms. Cycle 5: After refmac, R = 0.3007 (Rfree = 0.000) for 3000 atoms. Found 12 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 3119 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3134 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 9 peptides. Score 0.335 Round 2: 209 peptides, 36 chains. Longest chain 15 peptides. Score 0.404 Round 3: 212 peptides, 32 chains. Longest chain 14 peptides. Score 0.468 Round 4: 214 peptides, 31 chains. Longest chain 17 peptides. Score 0.488 Round 5: 217 peptides, 29 chains. Longest chain 24 peptides. Score 0.522 Taking the results from Round 5 Chains 29, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7139 restraints for refining 3092 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3174 (Rfree = 0.000) for 3092 atoms. Found 14 (19 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2962 (Rfree = 0.000) for 3043 atoms. Found 11 (19 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.2928 (Rfree = 0.000) for 3000 atoms. Found 16 (19 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.3135 (Rfree = 0.000) for 2972 atoms. Found 17 (19 requested) and removed 25 (9 requested) atoms. Cycle 10: After refmac, R = 0.2970 (Rfree = 0.000) for 2941 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3076 seeds are put forward Round 1: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.354 Round 2: 199 peptides, 30 chains. Longest chain 16 peptides. Score 0.455 Round 3: 207 peptides, 31 chains. Longest chain 14 peptides. Score 0.466 Round 4: 194 peptides, 30 chains. Longest chain 14 peptides. Score 0.440 Round 5: 217 peptides, 33 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 33, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6691 restraints for refining 2986 atoms. 5988 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3158 (Rfree = 0.000) for 2986 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 12: After refmac, R = 0.2919 (Rfree = 0.000) for 2945 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 13: After refmac, R = 0.2909 (Rfree = 0.000) for 2936 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.2882 (Rfree = 0.000) for 2912 atoms. Found 15 (18 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.2779 (Rfree = 0.000) for 2882 atoms. Found 11 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 3019 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3038 seeds are put forward Round 1: 172 peptides, 36 chains. Longest chain 15 peptides. Score 0.275 Round 2: 204 peptides, 36 chains. Longest chain 12 peptides. Score 0.388 Round 3: 212 peptides, 38 chains. Longest chain 10 peptides. Score 0.386 Round 4: 217 peptides, 36 chains. Longest chain 13 peptides. Score 0.430 Round 5: 231 peptides, 36 chains. Longest chain 13 peptides. Score 0.473 Taking the results from Round 5 Chains 36, Residues 195, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6609 restraints for refining 3063 atoms. 5824 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3021 (Rfree = 0.000) for 3063 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 17: After refmac, R = 0.2775 (Rfree = 0.000) for 3026 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.3116 (Rfree = 0.000) for 3014 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 19: After refmac, R = 0.3005 (Rfree = 0.000) for 2980 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 20: After refmac, R = 0.2879 (Rfree = 0.000) for 2954 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3138 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 8 peptides. Score 0.281 Round 2: 186 peptides, 31 chains. Longest chain 13 peptides. Score 0.400 Round 3: 185 peptides, 31 chains. Longest chain 13 peptides. Score 0.396 Round 4: 175 peptides, 31 chains. Longest chain 14 peptides. Score 0.362 Round 5: 175 peptides, 29 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 2 Chains 31, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6482 restraints for refining 2925 atoms. 5893 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2834 (Rfree = 0.000) for 2925 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2716 (Rfree = 0.000) for 2914 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2733 (Rfree = 0.000) for 2902 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.2851 (Rfree = 0.000) for 2897 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 25: After refmac, R = 0.2680 (Rfree = 0.000) for 2881 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 2990 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3010 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 11 peptides. Score 0.325 Round 2: 193 peptides, 30 chains. Longest chain 13 peptides. Score 0.437 Round 3: 199 peptides, 33 chains. Longest chain 13 peptides. Score 0.414 Round 4: 198 peptides, 29 chains. Longest chain 13 peptides. Score 0.466 Round 5: 206 peptides, 33 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 4 Chains 29, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6479 restraints for refining 2971 atoms. 5832 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2745 (Rfree = 0.000) for 2971 atoms. Found 16 (19 requested) and removed 27 (9 requested) atoms. Cycle 27: After refmac, R = 0.2447 (Rfree = 0.000) for 2939 atoms. Found 8 (18 requested) and removed 22 (9 requested) atoms. Cycle 28: After refmac, R = 0.2531 (Rfree = 0.000) for 2907 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2557 (Rfree = 0.000) for 2893 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 30: After refmac, R = 0.2575 (Rfree = 0.000) for 2884 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 2979 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2992 seeds are put forward Round 1: 153 peptides, 34 chains. Longest chain 7 peptides. Score 0.235 Round 2: 167 peptides, 31 chains. Longest chain 11 peptides. Score 0.334 Round 3: 172 peptides, 30 chains. Longest chain 16 peptides. Score 0.367 Round 4: 179 peptides, 32 chains. Longest chain 10 peptides. Score 0.361 Round 5: 179 peptides, 31 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 5 Chains 31, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6440 restraints for refining 2946 atoms. 5879 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2769 (Rfree = 0.000) for 2946 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 32: After refmac, R = 0.2588 (Rfree = 0.000) for 2921 atoms. Found 12 (18 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.2693 (Rfree = 0.000) for 2905 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 34: After refmac, R = 0.2465 (Rfree = 0.000) for 2895 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2378 (Rfree = 0.000) for 2893 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 2998 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3010 seeds are put forward Round 1: 129 peptides, 29 chains. Longest chain 6 peptides. Score 0.222 Round 2: 159 peptides, 32 chains. Longest chain 8 peptides. Score 0.289 Round 3: 169 peptides, 31 chains. Longest chain 13 peptides. Score 0.341 Round 4: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.345 Round 5: 161 peptides, 30 chains. Longest chain 13 peptides. Score 0.328 Taking the results from Round 4 Chains 31, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6704 restraints for refining 2989 atoms. 6179 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2525 (Rfree = 0.000) for 2989 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 37: After refmac, R = 0.2449 (Rfree = 0.000) for 2966 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 38: After refmac, R = 0.2407 (Rfree = 0.000) for 2955 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2598 (Rfree = 0.000) for 2950 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 40: After refmac, R = 0.2550 (Rfree = 0.000) for 2942 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3050 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 7 peptides. Score 0.210 Round 2: 154 peptides, 30 chains. Longest chain 10 peptides. Score 0.302 Round 3: 164 peptides, 31 chains. Longest chain 10 peptides. Score 0.323 Round 4: 159 peptides, 31 chains. Longest chain 10 peptides. Score 0.305 Round 5: 165 peptides, 30 chains. Longest chain 10 peptides. Score 0.342 Taking the results from Round 5 Chains 30, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6817 restraints for refining 3033 atoms. 6307 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3003 (Rfree = 0.000) for 3033 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 42: After refmac, R = 0.2781 (Rfree = 0.000) for 2983 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 43: After refmac, R = 0.2685 (Rfree = 0.000) for 2974 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.2622 (Rfree = 0.000) for 2968 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.2669 (Rfree = 0.000) for 2966 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.76 Search for helices and strands: 0 residues in 0 chains, 3047 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3059 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.223 Round 2: 124 peptides, 23 chains. Longest chain 10 peptides. Score 0.303 Round 3: 122 peptides, 23 chains. Longest chain 8 peptides. Score 0.295 Round 4: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.336 Round 5: 121 peptides, 22 chains. Longest chain 9 peptides. Score 0.308 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 103, 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 6605 restraints for refining 2939 atoms. 6214 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2748 (Rfree = 0.000) for 2939 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2836 (Rfree = 0.000) for 2920 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2713 (Rfree = 0.000) for 2896 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2695 (Rfree = 0.000) for 2883 atoms. TimeTaking 38.62