Mon 24 Dec 07:59:31 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 2i51-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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/2i51-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 07:59:35 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/2i51-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.2-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 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-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: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3120 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: 56.880 3.200 Wilson plot Bfac: 57.27 7279 reflections ( 85.94 % complete ) and 0 restraints for refining 3481 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3336 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2984 (Rfree = 0.000) for 3481 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.99 2.72 Search for helices and strands: 0 residues in 0 chains, 3509 seeds are put forward NCS extension: 0 residues added, 3509 seeds are put forward Round 1: 193 peptides, 37 chains. Longest chain 12 peptides. Score 0.337 Round 2: 196 peptides, 34 chains. Longest chain 14 peptides. Score 0.391 Round 3: 212 peptides, 34 chains. Longest chain 14 peptides. Score 0.443 Round 4: 235 peptides, 35 chains. Longest chain 17 peptides. Score 0.499 Round 5: 238 peptides, 34 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 5 Chains 34, Residues 204, Estimated correctness of the model 17.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6116 restraints for refining 2848 atoms. 5334 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2704 (Rfree = 0.000) for 2848 atoms. Found 17 (25 requested) and removed 18 (12 requested) atoms. Cycle 2: After refmac, R = 0.2658 (Rfree = 0.000) for 2824 atoms. Found 14 (25 requested) and removed 13 (12 requested) atoms. Cycle 3: After refmac, R = 0.2613 (Rfree = 0.000) for 2812 atoms. Found 16 (25 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2591 (Rfree = 0.000) for 2811 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2484 (Rfree = 0.000) for 2798 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 2870 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2898 seeds are put forward Round 1: 209 peptides, 36 chains. Longest chain 12 peptides. Score 0.405 Round 2: 227 peptides, 35 chains. Longest chain 18 peptides. Score 0.475 Round 3: 241 peptides, 37 chains. Longest chain 20 peptides. Score 0.491 Round 4: 257 peptides, 40 chains. Longest chain 19 peptides. Score 0.499 Round 5: 242 peptides, 34 chains. Longest chain 19 peptides. Score 0.531 Taking the results from Round 5 Chains 37, Residues 208, Estimated correctness of the model 21.1 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5962 restraints for refining 2848 atoms. 5078 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2665 (Rfree = 0.000) for 2848 atoms. Found 18 (25 requested) and removed 18 (12 requested) atoms. Cycle 7: After refmac, R = 0.2524 (Rfree = 0.000) for 2831 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 8: After refmac, R = 0.2555 (Rfree = 0.000) for 2817 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2495 (Rfree = 0.000) for 2806 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.2455 (Rfree = 0.000) for 2794 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 2832 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2844 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 14 peptides. Score 0.375 Round 2: 242 peptides, 33 chains. Longest chain 19 peptides. Score 0.543 Round 3: 246 peptides, 36 chains. Longest chain 19 peptides. Score 0.518 Round 4: 254 peptides, 34 chains. Longest chain 19 peptides. Score 0.564 Round 5: 263 peptides, 37 chains. Longest chain 14 peptides. Score 0.552 Taking the results from Round 4 Chains 34, Residues 220, Estimated correctness of the model 31.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5886 restraints for refining 2848 atoms. 4977 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2568 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. Cycle 12: After refmac, R = 0.2394 (Rfree = 0.000) for 2850 atoms. Found 12 (25 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.2338 (Rfree = 0.000) for 2845 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.2355 (Rfree = 0.000) for 2829 atoms. Found 8 (25 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.2329 (Rfree = 0.000) for 2817 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 2880 seeds are put forward Round 1: 228 peptides, 39 chains. Longest chain 16 peptides. Score 0.425 Round 2: 250 peptides, 35 chains. Longest chain 19 peptides. Score 0.541 Round 3: 254 peptides, 36 chains. Longest chain 19 peptides. Score 0.540 Round 4: 269 peptides, 36 chains. Longest chain 20 peptides. Score 0.579 Round 5: 248 peptides, 30 chains. Longest chain 20 peptides. Score 0.595 Taking the results from Round 5 Chains 30, Residues 218, Estimated correctness of the model 39.7 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 5824 restraints for refining 2848 atoms. 4846 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2577 (Rfree = 0.000) for 2848 atoms. Found 20 (25 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.2370 (Rfree = 0.000) for 2846 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2345 (Rfree = 0.000) for 2839 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2303 (Rfree = 0.000) for 2829 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2295 (Rfree = 0.000) for 2821 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 2859 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2876 seeds are put forward Round 1: 235 peptides, 42 chains. Longest chain 14 peptides. Score 0.406 Round 2: 235 peptides, 37 chains. Longest chain 20 peptides. Score 0.473 Round 3: 252 peptides, 40 chains. Longest chain 20 peptides. Score 0.485 Round 4: 234 peptides, 35 chains. Longest chain 22 peptides. Score 0.496 Round 5: 238 peptides, 34 chains. Longest chain 14 peptides. Score 0.520 Taking the results from Round 5 Chains 34, Residues 204, Estimated correctness of the model 17.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6334 restraints for refining 2848 atoms. 5552 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2449 (Rfree = 0.000) for 2848 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. Cycle 22: After refmac, R = 0.2254 (Rfree = 0.000) for 2847 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2172 (Rfree = 0.000) for 2839 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2122 (Rfree = 0.000) for 2834 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2073 (Rfree = 0.000) for 2829 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2867 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2887 seeds are put forward Round 1: 195 peptides, 34 chains. Longest chain 21 peptides. Score 0.387 Round 2: 211 peptides, 31 chains. Longest chain 19 peptides. Score 0.480 Round 3: 215 peptides, 30 chains. Longest chain 19 peptides. Score 0.505 Round 4: 220 peptides, 30 chains. Longest chain 24 peptides. Score 0.520 Round 5: 212 peptides, 31 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 4 Chains 30, Residues 190, Estimated correctness of the model 17.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6369 restraints for refining 2846 atoms. 5639 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2417 (Rfree = 0.000) for 2846 atoms. Found 17 (25 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.2308 (Rfree = 0.000) for 2840 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2233 (Rfree = 0.000) for 2838 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2181 (Rfree = 0.000) for 2832 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.2119 (Rfree = 0.000) for 2828 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2888 seeds are put forward Round 1: 189 peptides, 31 chains. Longest chain 14 peptides. Score 0.411 Round 2: 196 peptides, 30 chains. Longest chain 14 peptides. Score 0.447 Round 3: 194 peptides, 32 chains. Longest chain 15 peptides. Score 0.413 Round 4: 209 peptides, 33 chains. Longest chain 15 peptides. Score 0.447 Round 5: 192 peptides, 28 chains. Longest chain 16 peptides. Score 0.463 Taking the results from Round 5 Chains 28, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6450 restraints for refining 2848 atoms. 5822 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2364 (Rfree = 0.000) for 2848 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. Cycle 32: After refmac, R = 0.2296 (Rfree = 0.000) for 2850 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.2286 (Rfree = 0.000) for 2845 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2202 (Rfree = 0.000) for 2840 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2165 (Rfree = 0.000) for 2831 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 2865 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2885 seeds are put forward Round 1: 189 peptides, 33 chains. Longest chain 13 peptides. Score 0.382 Round 2: 189 peptides, 31 chains. Longest chain 15 peptides. Score 0.411 Round 3: 193 peptides, 29 chains. Longest chain 16 peptides. Score 0.452 Round 4: 202 peptides, 29 chains. Longest chain 17 peptides. Score 0.480 Round 5: 192 peptides, 30 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 4 Chains 29, Residues 173, Estimated correctness of the model 4.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6427 restraints for refining 2848 atoms. 5750 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 2848 atoms. Found 13 (25 requested) and removed 25 (12 requested) atoms. Cycle 37: After refmac, R = 0.2225 (Rfree = 0.000) for 2832 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2112 (Rfree = 0.000) for 2830 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2068 (Rfree = 0.000) for 2824 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2040 (Rfree = 0.000) for 2814 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2874 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 12 peptides. Score 0.370 Round 2: 198 peptides, 30 chains. Longest chain 12 peptides. Score 0.454 Round 3: 187 peptides, 29 chains. Longest chain 19 peptides. Score 0.433 Round 4: 196 peptides, 31 chains. Longest chain 13 peptides. Score 0.433 Round 5: 185 peptides, 29 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 2 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7279 reflections ( 85.94 % complete ) and 6385 restraints for refining 2847 atoms. 5743 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2191 (Rfree = 0.000) for 2847 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.2129 (Rfree = 0.000) for 2838 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2049 (Rfree = 0.000) for 2827 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2036 (Rfree = 0.000) for 2817 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2006 (Rfree = 0.000) for 2813 atoms. Found 1 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2861 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 10 peptides. Score 0.320 Round 2: 167 peptides, 26 chains. Longest chain 15 peptides. Score 0.411 Round 3: 174 peptides, 25 chains. Longest chain 15 peptides. Score 0.448 Round 4: 174 peptides, 27 chains. Longest chain 15 peptides. Score 0.419 Round 5: 173 peptides, 25 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 149, 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 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7279 reflections ( 85.94 % complete ) and 6478 restraints for refining 2848 atoms. 5907 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2233 (Rfree = 0.000) for 2848 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2209 (Rfree = 0.000) for 2832 atoms. Found 0 (25 requested) and removed 6 (12 requested) atoms. Cycle 48: After refmac, R = 0.2223 (Rfree = 0.000) for 2821 atoms. Found 0 (25 requested) and removed 7 (12 requested) atoms. Cycle 49: After refmac, R = 0.2162 (Rfree = 0.000) for 2813 atoms. TimeTaking 37.35