Mon 24 Dec 00:36:36 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 2a6a-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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/2a6a-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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 00:36:41 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/2a6a-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-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 323 and 0 Target number of residues in the AU: 323 Target solvent content: 0.6681 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 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: 108.588 3.600 Wilson plot Bfac: 90.78 6404 reflections ( 98.81 % complete ) and 0 restraints for refining 3855 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3443 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 3855 atoms. Found 24 (24 requested) and removed 44 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.43 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 0 residues added, 3903 seeds are put forward Round 1: 178 peptides, 32 chains. Longest chain 12 peptides. Score 0.348 Round 2: 218 peptides, 33 chains. Longest chain 14 peptides. Score 0.457 Round 3: 251 peptides, 34 chains. Longest chain 17 peptides. Score 0.535 Round 4: 243 peptides, 29 chains. Longest chain 22 peptides. Score 0.571 Round 5: 248 peptides, 31 chains. Longest chain 19 peptides. Score 0.561 Taking the results from Round 4 Chains 31, Residues 214, Estimated correctness of the model 3.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 7165 restraints for refining 3162 atoms. 6300 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2602 (Rfree = 0.000) for 3162 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 2: After refmac, R = 0.2408 (Rfree = 0.000) for 3090 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 3: After refmac, R = 0.2751 (Rfree = 0.000) for 3050 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 4: After refmac, R = 0.2294 (Rfree = 0.000) for 3035 atoms. Found 14 (19 requested) and removed 20 (9 requested) atoms. Cycle 5: After refmac, R = 0.2141 (Rfree = 0.000) for 3006 atoms. Found 9 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3100 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 3131 seeds are put forward Round 1: 211 peptides, 33 chains. Longest chain 15 peptides. Score 0.437 Round 2: 223 peptides, 33 chains. Longest chain 16 peptides. Score 0.471 Round 3: 253 peptides, 32 chains. Longest chain 18 peptides. Score 0.562 Round 4: 251 peptides, 35 chains. Longest chain 17 peptides. Score 0.523 Round 5: 244 peptides, 30 chains. Longest chain 18 peptides. Score 0.563 Taking the results from Round 5 Chains 30, Residues 214, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6725 restraints for refining 3110 atoms. 5838 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2389 (Rfree = 0.000) for 3110 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 7: After refmac, R = 0.2781 (Rfree = 0.000) for 3072 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 3040 atoms. Found 17 (19 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2070 (Rfree = 0.000) for 3009 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2709 (Rfree = 0.000) for 2995 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 3153 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3175 seeds are put forward Round 1: 226 peptides, 37 chains. Longest chain 16 peptides. Score 0.430 Round 2: 240 peptides, 29 chains. Longest chain 20 peptides. Score 0.564 Round 3: 256 peptides, 33 chains. Longest chain 17 peptides. Score 0.559 Round 4: 230 peptides, 26 chains. Longest chain 17 peptides. Score 0.574 Round 5: 226 peptides, 29 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 4 Chains 28, Residues 204, Estimated correctness of the model 4.2 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6552 restraints for refining 3058 atoms. 5699 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2381 (Rfree = 0.000) for 3058 atoms. Found 15 (19 requested) and removed 63 (9 requested) atoms. Cycle 12: After refmac, R = 0.2278 (Rfree = 0.000) for 2982 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 13: After refmac, R = 0.2100 (Rfree = 0.000) for 2960 atoms. Found 16 (19 requested) and removed 25 (9 requested) atoms. Cycle 14: After refmac, R = 0.2135 (Rfree = 0.000) for 2938 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.2133 (Rfree = 0.000) for 2926 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.45 Search for helices and strands: 0 residues in 0 chains, 3037 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3055 seeds are put forward Round 1: 218 peptides, 36 chains. Longest chain 17 peptides. Score 0.419 Round 2: 226 peptides, 33 chains. Longest chain 19 peptides. Score 0.480 Round 3: 229 peptides, 32 chains. Longest chain 15 peptides. Score 0.500 Round 4: 246 peptides, 34 chains. Longest chain 15 peptides. Score 0.522 Round 5: 238 peptides, 29 chains. Longest chain 16 peptides. Score 0.559 Taking the results from Round 5 Chains 30, Residues 209, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6998 restraints for refining 3125 atoms. 6157 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2211 (Rfree = 0.000) for 3125 atoms. Found 17 (20 requested) and removed 53 (10 requested) atoms. Cycle 17: After refmac, R = 0.2103 (Rfree = 0.000) for 3058 atoms. Found 8 (19 requested) and removed 25 (9 requested) atoms. Cycle 18: After refmac, R = 0.2106 (Rfree = 0.000) for 3028 atoms. Found 15 (19 requested) and removed 18 (9 requested) atoms. Cycle 19: After refmac, R = 0.2085 (Rfree = 0.000) for 3014 atoms. Found 10 (19 requested) and removed 13 (9 requested) atoms. Cycle 20: After refmac, R = 0.2124 (Rfree = 0.000) for 3000 atoms. Found 15 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.44 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3139 seeds are put forward Round 1: 203 peptides, 33 chains. Longest chain 20 peptides. Score 0.413 Round 2: 223 peptides, 33 chains. Longest chain 17 peptides. Score 0.471 Round 3: 227 peptides, 34 chains. Longest chain 14 peptides. Score 0.470 Round 4: 239 peptides, 34 chains. Longest chain 22 peptides. Score 0.503 Round 5: 239 peptides, 32 chains. Longest chain 22 peptides. Score 0.527 Taking the results from Round 5 Chains 35, Residues 207, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6795 restraints for refining 3162 atoms. 5916 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2346 (Rfree = 0.000) for 3162 atoms. Found 17 (20 requested) and removed 47 (10 requested) atoms. Cycle 22: After refmac, R = 0.2232 (Rfree = 0.000) for 3107 atoms. Found 14 (20 requested) and removed 25 (10 requested) atoms. Cycle 23: After refmac, R = 0.2189 (Rfree = 0.000) for 3086 atoms. Found 13 (19 requested) and removed 25 (9 requested) atoms. Cycle 24: After refmac, R = 0.2403 (Rfree = 0.000) for 3060 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 25: After refmac, R = 0.2060 (Rfree = 0.000) for 3030 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3118 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3130 seeds are put forward Round 1: 194 peptides, 32 chains. Longest chain 16 peptides. Score 0.399 Round 2: 206 peptides, 31 chains. Longest chain 12 peptides. Score 0.448 Round 3: 223 peptides, 32 chains. Longest chain 22 peptides. Score 0.484 Round 4: 214 peptides, 31 chains. Longest chain 21 peptides. Score 0.471 Round 5: 220 peptides, 32 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 3 Chains 32, Residues 191, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6995 restraints for refining 3098 atoms. 6247 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2333 (Rfree = 0.000) for 3098 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 27: After refmac, R = 0.2112 (Rfree = 0.000) for 3060 atoms. Found 13 (19 requested) and removed 22 (9 requested) atoms. Cycle 28: After refmac, R = 0.2165 (Rfree = 0.000) for 3037 atoms. Found 17 (19 requested) and removed 22 (9 requested) atoms. Cycle 29: After refmac, R = 0.2556 (Rfree = 0.000) for 3019 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 30: After refmac, R = 0.2393 (Rfree = 0.000) for 2986 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 3108 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3133 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 8 peptides. Score 0.256 Round 2: 202 peptides, 35 chains. Longest chain 14 peptides. Score 0.383 Round 3: 208 peptides, 32 chains. Longest chain 13 peptides. Score 0.441 Round 4: 213 peptides, 33 chains. Longest chain 20 peptides. Score 0.443 Round 5: 211 peptides, 30 chains. Longest chain 23 peptides. Score 0.475 Taking the results from Round 5 Chains 30, Residues 181, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6957 restraints for refining 3124 atoms. 6250 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2281 (Rfree = 0.000) for 3124 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 32: After refmac, R = 0.2279 (Rfree = 0.000) for 3090 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 33: After refmac, R = 0.2183 (Rfree = 0.000) for 3070 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 34: After refmac, R = 0.2152 (Rfree = 0.000) for 3057 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.2076 (Rfree = 0.000) for 3050 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3194 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 12 peptides. Score 0.288 Round 2: 194 peptides, 32 chains. Longest chain 14 peptides. Score 0.399 Round 3: 202 peptides, 32 chains. Longest chain 16 peptides. Score 0.423 Round 4: 210 peptides, 34 chains. Longest chain 19 peptides. Score 0.421 Round 5: 210 peptides, 32 chains. Longest chain 19 peptides. Score 0.447 Taking the results from Round 5 Chains 32, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 7021 restraints for refining 3146 atoms. 6341 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2290 (Rfree = 0.000) for 3146 atoms. Found 20 (20 requested) and removed 40 (10 requested) atoms. Cycle 37: After refmac, R = 0.2149 (Rfree = 0.000) for 3109 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 38: After refmac, R = 0.2135 (Rfree = 0.000) for 3089 atoms. Found 18 (19 requested) and removed 29 (9 requested) atoms. Cycle 39: After refmac, R = 0.2072 (Rfree = 0.000) for 3065 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.1983 (Rfree = 0.000) for 3057 atoms. Found 18 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3184 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 10 peptides. Score 0.274 Round 2: 198 peptides, 34 chains. Longest chain 22 peptides. Score 0.384 Round 3: 187 peptides, 31 chains. Longest chain 14 peptides. Score 0.391 Round 4: 194 peptides, 30 chains. Longest chain 15 peptides. Score 0.426 Round 5: 177 peptides, 28 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 4 Chains 30, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6752 restraints for refining 3062 atoms. 6126 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2348 (Rfree = 0.000) for 3062 atoms. Found 19 (19 requested) and removed 46 (9 requested) atoms. Cycle 42: After refmac, R = 0.2344 (Rfree = 0.000) for 3014 atoms. Found 15 (19 requested) and removed 63 (9 requested) atoms. Cycle 43: After refmac, R = 0.2750 (Rfree = 0.000) for 2955 atoms. Found 19 (19 requested) and removed 52 (9 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 2911 atoms. Found 14 (18 requested) and removed 22 (9 requested) atoms. Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 2892 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.43 Search for helices and strands: 0 residues in 0 chains, 3000 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3019 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 8 peptides. Score 0.218 Round 2: 143 peptides, 27 chains. Longest chain 10 peptides. Score 0.302 Round 3: 154 peptides, 28 chains. Longest chain 16 peptides. Score 0.325 Round 4: 164 peptides, 31 chains. Longest chain 9 peptides. Score 0.315 Round 5: 158 peptides, 29 chains. Longest chain 11 peptides. Score 0.324 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 126, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (126 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6404 reflections ( 98.81 % complete ) and 6472 restraints for refining 2890 atoms. 5987 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2109 (Rfree = 0.000) for 2890 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2939 (Rfree = 0.000) for 2872 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1921 (Rfree = 0.000) for 2856 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2065 (Rfree = 0.000) for 2834 atoms. TimeTaking 45.95