Sun 23 Dec 22:23:10 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 2i51-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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/2i51-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 22:23:19 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/2i51-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 349 and 0 Target number of residues in the AU: 349 Target solvent content: 0.6114 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-3.2-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: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.85 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: 56.880 3.200 Wilson plot Bfac: 57.27 7279 reflections ( 85.94 % complete ) and 0 restraints for refining 3454 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2712 (Rfree = 0.000) for 3454 atoms. Found 30 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 0 residues added, 3511 seeds are put forward Round 1: 187 peptides, 31 chains. Longest chain 21 peptides. Score 0.404 Round 2: 220 peptides, 32 chains. Longest chain 27 peptides. Score 0.494 Round 3: 227 peptides, 34 chains. Longest chain 27 peptides. Score 0.488 Round 4: 255 peptides, 30 chains. Longest chain 27 peptides. Score 0.612 Round 5: 248 peptides, 32 chains. Longest chain 30 peptides. Score 0.571 Taking the results from Round 4 Chains 33, Residues 225, Estimated correctness of the model 44.3 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5444 restraints for refining 2861 atoms. 4387 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 2861 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2502 (Rfree = 0.000) for 2847 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 3: After refmac, R = 0.2434 (Rfree = 0.000) for 2834 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2460 (Rfree = 0.000) for 2817 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.2470 (Rfree = 0.000) for 2814 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 2878 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2904 seeds are put forward Round 1: 230 peptides, 36 chains. Longest chain 19 peptides. Score 0.471 Round 2: 254 peptides, 31 chains. Longest chain 28 peptides. Score 0.598 Round 3: 239 peptides, 33 chains. Longest chain 25 peptides. Score 0.535 Round 4: 236 peptides, 32 chains. Longest chain 25 peptides. Score 0.539 Round 5: 239 peptides, 33 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 2 Chains 33, Residues 223, Estimated correctness of the model 40.5 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5991 restraints for refining 2847 atoms. 5068 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2499 (Rfree = 0.000) for 2847 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 7: After refmac, R = 0.2342 (Rfree = 0.000) for 2849 atoms. Found 4 (25 requested) and removed 14 (12 requested) atoms. Cycle 8: After refmac, R = 0.2554 (Rfree = 0.000) for 2829 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 9: After refmac, R = 0.2194 (Rfree = 0.000) for 2832 atoms. Found 4 (25 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2159 (Rfree = 0.000) for 2817 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2880 seeds are put forward NCS extension: 42 residues added (7 deleted due to clashes), 2922 seeds are put forward Round 1: 225 peptides, 34 chains. Longest chain 24 peptides. Score 0.482 Round 2: 253 peptides, 30 chains. Longest chain 26 peptides. Score 0.607 Round 3: 266 peptides, 30 chains. Longest chain 27 peptides. Score 0.637 Round 4: 275 peptides, 34 chains. Longest chain 28 peptides. Score 0.616 Round 5: 244 peptides, 31 chains. Longest chain 22 peptides. Score 0.573 Taking the results from Round 3 Chains 30, Residues 236, Estimated correctness of the model 50.7 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5756 restraints for refining 2848 atoms. 4745 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2504 (Rfree = 0.000) for 2848 atoms. Found 14 (25 requested) and removed 18 (12 requested) atoms. Cycle 12: After refmac, R = 0.2389 (Rfree = 0.000) for 2836 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 13: After refmac, R = 0.2349 (Rfree = 0.000) for 2827 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 2817 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.2293 (Rfree = 0.000) for 2809 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2874 seeds are put forward NCS extension: 26 residues added (8 deleted due to clashes), 2900 seeds are put forward Round 1: 229 peptides, 29 chains. Longest chain 31 peptides. Score 0.557 Round 2: 241 peptides, 27 chains. Longest chain 27 peptides. Score 0.611 Round 3: 245 peptides, 28 chains. Longest chain 30 peptides. Score 0.610 Round 4: 247 peptides, 26 chains. Longest chain 33 peptides. Score 0.636 Round 5: 250 peptides, 29 chains. Longest chain 24 peptides. Score 0.611 Taking the results from Round 4 Chains 28, Residues 221, Estimated correctness of the model 50.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7279 reflections ( 85.94 % complete ) and 5984 restraints for refining 2848 atoms. 5051 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2573 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 17: After refmac, R = 0.2401 (Rfree = 0.000) for 2852 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2339 (Rfree = 0.000) for 2851 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2310 (Rfree = 0.000) for 2844 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 2834 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2882 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 2924 seeds are put forward Round 1: 217 peptides, 33 chains. Longest chain 20 peptides. Score 0.471 Round 2: 243 peptides, 32 chains. Longest chain 31 peptides. Score 0.558 Round 3: 249 peptides, 30 chains. Longest chain 34 peptides. Score 0.597 Round 4: 251 peptides, 31 chains. Longest chain 21 peptides. Score 0.591 Round 5: 241 peptides, 30 chains. Longest chain 22 peptides. Score 0.577 Taking the results from Round 3 Chains 33, Residues 219, Estimated correctness of the model 40.2 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5680 restraints for refining 2847 atoms. 4617 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2550 (Rfree = 0.000) for 2847 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.2413 (Rfree = 0.000) for 2836 atoms. Found 6 (25 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2398 (Rfree = 0.000) for 2826 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2370 (Rfree = 0.000) for 2817 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2310 (Rfree = 0.000) for 2810 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 2878 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2908 seeds are put forward Round 1: 217 peptides, 31 chains. Longest chain 27 peptides. Score 0.498 Round 2: 230 peptides, 27 chains. Longest chain 34 peptides. Score 0.584 Round 3: 232 peptides, 25 chains. Longest chain 21 peptides. Score 0.612 Round 4: 242 peptides, 29 chains. Longest chain 23 peptides. Score 0.591 Round 5: 224 peptides, 26 chains. Longest chain 26 peptides. Score 0.580 Taking the results from Round 3 Chains 25, Residues 207, Estimated correctness of the model 44.3 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5714 restraints for refining 2848 atoms. 4728 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2425 (Rfree = 0.000) for 2848 atoms. Found 15 (25 requested) and removed 13 (12 requested) atoms. Cycle 27: After refmac, R = 0.2254 (Rfree = 0.000) for 2842 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 2834 atoms. Found 14 (25 requested) and removed 14 (12 requested) atoms. Cycle 29: After refmac, R = 0.2220 (Rfree = 0.000) for 2827 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.2189 (Rfree = 0.000) for 2822 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.79 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 34 residues added (4 deleted due to clashes), 2896 seeds are put forward Round 1: 213 peptides, 33 chains. Longest chain 19 peptides. Score 0.459 Round 2: 229 peptides, 32 chains. Longest chain 20 peptides. Score 0.520 Round 3: 222 peptides, 29 chains. Longest chain 17 peptides. Score 0.538 Round 4: 231 peptides, 30 chains. Longest chain 21 peptides. Score 0.550 Round 5: 227 peptides, 32 chains. Longest chain 26 peptides. Score 0.514 Taking the results from Round 4 Chains 30, Residues 201, Estimated correctness of the model 26.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5960 restraints for refining 2847 atoms. 5106 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 2847 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 32: After refmac, R = 0.2274 (Rfree = 0.000) for 2851 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.2249 (Rfree = 0.000) for 2841 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2202 (Rfree = 0.000) for 2840 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2179 (Rfree = 0.000) for 2833 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 2869 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 2902 seeds are put forward Round 1: 217 peptides, 38 chains. Longest chain 17 peptides. Score 0.403 Round 2: 223 peptides, 29 chains. Longest chain 25 peptides. Score 0.541 Round 3: 217 peptides, 28 chains. Longest chain 15 peptides. Score 0.537 Round 4: 212 peptides, 25 chains. Longest chain 25 peptides. Score 0.560 Round 5: 216 peptides, 28 chains. Longest chain 20 peptides. Score 0.534 Taking the results from Round 4 Chains 25, Residues 187, Estimated correctness of the model 29.8 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6014 restraints for refining 2848 atoms. 5191 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2388 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2197 (Rfree = 0.000) for 2858 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2156 (Rfree = 0.000) for 2854 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2125 (Rfree = 0.000) for 2845 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2181 (Rfree = 0.000) for 2844 atoms. Found 17 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2932 seeds are put forward Round 1: 182 peptides, 27 chains. Longest chain 20 peptides. Score 0.445 Round 2: 214 peptides, 30 chains. Longest chain 18 peptides. Score 0.502 Round 3: 215 peptides, 27 chains. Longest chain 24 peptides. Score 0.544 Round 4: 210 peptides, 27 chains. Longest chain 21 peptides. Score 0.530 Round 5: 207 peptides, 25 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 5 Chains 25, Residues 182, Estimated correctness of the model 26.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6330 restraints for refining 2848 atoms. 5598 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2407 (Rfree = 0.000) for 2848 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.2286 (Rfree = 0.000) for 2849 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.2285 (Rfree = 0.000) for 2851 atoms. Found 14 (25 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.2202 (Rfree = 0.000) for 2849 atoms. Found 16 (25 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2026 (Rfree = 0.000) for 2851 atoms. Found 2 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 2888 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2916 seeds are put forward Round 1: 187 peptides, 30 chains. Longest chain 16 peptides. Score 0.418 Round 2: 217 peptides, 29 chains. Longest chain 20 peptides. Score 0.524 Round 3: 218 peptides, 28 chains. Longest chain 20 peptides. Score 0.539 Round 4: 215 peptides, 29 chains. Longest chain 18 peptides. Score 0.518 Round 5: 210 peptides, 31 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 190, Estimated correctness of the model 23.6 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7279 reflections ( 85.94 % complete ) and 6192 restraints for refining 2848 atoms. 5421 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2200 (Rfree = 0.000) for 2848 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2228 (Rfree = 0.000) for 2832 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2220 (Rfree = 0.000) for 2816 atoms. Found 0 (25 requested) and removed 11 (12 requested) atoms. Cycle 49: After refmac, R = 0.2202 (Rfree = 0.000) for 2802 atoms. TimeTaking 51.38