null Mon 24 Dec 00:27:33 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 2fna-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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/2fna-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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 00:27:37 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/2fna-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-4.0-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6787 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-4.0-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: 4 Cell parameters: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5712 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: 69.461 4.000 Wilson plot Bfac: 99.62 6907 reflections ( 98.46 % complete ) and 0 restraints for refining 6296 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3380 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3361 (Rfree = 0.000) for 6296 atoms. Found 29 (29 requested) and removed 56 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.73 Search for helices and strands: 0 residues in 0 chains, 6417 seeds are put forward NCS extension: 0 residues added, 6417 seeds are put forward Round 1: 231 peptides, 45 chains. Longest chain 10 peptides. Score 0.291 Round 2: 262 peptides, 44 chains. Longest chain 15 peptides. Score 0.367 Round 3: 296 peptides, 48 chains. Longest chain 16 peptides. Score 0.400 Round 4: 299 peptides, 45 chains. Longest chain 17 peptides. Score 0.431 Round 5: 299 peptides, 45 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 5 Chains 45, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12614 restraints for refining 5156 atoms. 11643 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2939 (Rfree = 0.000) for 5156 atoms. Found 24 (24 requested) and removed 37 (12 requested) atoms. Cycle 2: After refmac, R = 0.2956 (Rfree = 0.000) for 5043 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 3: After refmac, R = 0.2772 (Rfree = 0.000) for 4955 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 4: After refmac, R = 0.2560 (Rfree = 0.000) for 4858 atoms. Found 20 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.2785 (Rfree = 0.000) for 4809 atoms. Found 17 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.93 3.73 Search for helices and strands: 0 residues in 0 chains, 4980 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5001 seeds are put forward Round 1: 243 peptides, 50 chains. Longest chain 13 peptides. Score 0.270 Round 2: 283 peptides, 49 chains. Longest chain 15 peptides. Score 0.365 Round 3: 305 peptides, 49 chains. Longest chain 16 peptides. Score 0.409 Round 4: 300 peptides, 46 chains. Longest chain 21 peptides. Score 0.425 Round 5: 308 peptides, 49 chains. Longest chain 22 peptides. Score 0.415 Taking the results from Round 4 Chains 46, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11341 restraints for refining 4775 atoms. 10371 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2881 (Rfree = 0.000) for 4775 atoms. Found 22 (22 requested) and removed 65 (11 requested) atoms. Cycle 7: After refmac, R = 0.2709 (Rfree = 0.000) for 4654 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 8: After refmac, R = 0.2190 (Rfree = 0.000) for 4598 atoms. Found 14 (22 requested) and removed 29 (11 requested) atoms. Cycle 9: After refmac, R = 0.2556 (Rfree = 0.000) for 4559 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 10: After refmac, R = 0.2473 (Rfree = 0.000) for 4535 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.91 3.71 Search for helices and strands: 0 residues in 0 chains, 4723 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 4755 seeds are put forward Round 1: 275 peptides, 51 chains. Longest chain 14 peptides. Score 0.330 Round 2: 288 peptides, 46 chains. Longest chain 15 peptides. Score 0.401 Round 3: 306 peptides, 46 chains. Longest chain 15 peptides. Score 0.436 Round 4: 316 peptides, 43 chains. Longest chain 20 peptides. Score 0.479 Round 5: 304 peptides, 43 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 4 Chains 43, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11307 restraints for refining 4921 atoms. 10258 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2715 (Rfree = 0.000) for 4921 atoms. Found 23 (23 requested) and removed 52 (11 requested) atoms. Cycle 12: After refmac, R = 0.2358 (Rfree = 0.000) for 4831 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 13: After refmac, R = 0.2194 (Rfree = 0.000) for 4776 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 14: After refmac, R = 0.1965 (Rfree = 0.000) for 4740 atoms. Found 11 (22 requested) and removed 18 (11 requested) atoms. Cycle 15: After refmac, R = 0.1974 (Rfree = 0.000) for 4707 atoms. Found 16 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.64 Search for helices and strands: 0 residues in 0 chains, 4907 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4934 seeds are put forward Round 1: 274 peptides, 54 chains. Longest chain 9 peptides. Score 0.301 Round 2: 327 peptides, 51 chains. Longest chain 11 peptides. Score 0.434 Round 3: 328 peptides, 48 chains. Longest chain 16 peptides. Score 0.460 Round 4: 320 peptides, 49 chains. Longest chain 14 peptides. Score 0.437 Round 5: 325 peptides, 46 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 5 Chains 46, Residues 279, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11726 restraints for refining 5123 atoms. 10656 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2465 (Rfree = 0.000) for 5123 atoms. Found 24 (24 requested) and removed 47 (12 requested) atoms. Cycle 17: After refmac, R = 0.2267 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 18: After refmac, R = 0.2092 (Rfree = 0.000) for 5022 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.2251 (Rfree = 0.000) for 5002 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 20: After refmac, R = 0.2040 (Rfree = 0.000) for 4992 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.92 3.72 Search for helices and strands: 0 residues in 0 chains, 5172 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5186 seeds are put forward Round 1: 247 peptides, 49 chains. Longest chain 10 peptides. Score 0.288 Round 2: 281 peptides, 48 chains. Longest chain 13 peptides. Score 0.370 Round 3: 292 peptides, 47 chains. Longest chain 14 peptides. Score 0.401 Round 4: 290 peptides, 47 chains. Longest chain 12 peptides. Score 0.397 Round 5: 305 peptides, 49 chains. Longest chain 15 peptides. Score 0.409 Taking the results from Round 5 Chains 49, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 11977 restraints for refining 5157 atoms. 11002 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2272 (Rfree = 0.000) for 5157 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 5108 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 23: After refmac, R = 0.2010 (Rfree = 0.000) for 5077 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 24: After refmac, R = 0.1842 (Rfree = 0.000) for 5064 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 25: After refmac, R = 0.1784 (Rfree = 0.000) for 5054 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.64 Search for helices and strands: 0 residues in 0 chains, 5218 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5235 seeds are put forward Round 1: 243 peptides, 47 chains. Longest chain 11 peptides. Score 0.298 Round 2: 275 peptides, 48 chains. Longest chain 13 peptides. Score 0.357 Round 3: 282 peptides, 45 chains. Longest chain 13 peptides. Score 0.398 Round 4: 266 peptides, 46 chains. Longest chain 13 peptides. Score 0.357 Round 5: 280 peptides, 44 chains. Longest chain 16 peptides. Score 0.403 Taking the results from Round 5 Chains 44, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12215 restraints for refining 5158 atoms. 11315 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2203 (Rfree = 0.000) for 5158 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 27: After refmac, R = 0.2024 (Rfree = 0.000) for 5098 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 28: After refmac, R = 0.1895 (Rfree = 0.000) for 5069 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 29: After refmac, R = 0.2052 (Rfree = 0.000) for 5048 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 30: After refmac, R = 0.1875 (Rfree = 0.000) for 5033 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 5164 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5175 seeds are put forward Round 1: 232 peptides, 50 chains. Longest chain 9 peptides. Score 0.245 Round 2: 264 peptides, 49 chains. Longest chain 15 peptides. Score 0.325 Round 3: 270 peptides, 46 chains. Longest chain 14 peptides. Score 0.365 Round 4: 287 peptides, 50 chains. Longest chain 15 peptides. Score 0.364 Round 5: 283 peptides, 49 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Chains 49, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12077 restraints for refining 5158 atoms. 11190 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2029 (Rfree = 0.000) for 5158 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 32: After refmac, R = 0.2098 (Rfree = 0.000) for 5117 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 33: After refmac, R = 0.1965 (Rfree = 0.000) for 5097 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 34: After refmac, R = 0.1745 (Rfree = 0.000) for 5081 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.2038 (Rfree = 0.000) for 5077 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.67 Search for helices and strands: 0 residues in 0 chains, 5233 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5246 seeds are put forward Round 1: 221 peptides, 49 chains. Longest chain 7 peptides. Score 0.228 Round 2: 259 peptides, 50 chains. Longest chain 10 peptides. Score 0.305 Round 3: 256 peptides, 46 chains. Longest chain 11 peptides. Score 0.336 Round 4: 246 peptides, 42 chains. Longest chain 13 peptides. Score 0.352 Round 5: 244 peptides, 47 chains. Longest chain 11 peptides. Score 0.300 Taking the results from Round 4 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12473 restraints for refining 5158 atoms. 11699 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 5158 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 37: After refmac, R = 0.1997 (Rfree = 0.000) for 5124 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 38: After refmac, R = 0.1952 (Rfree = 0.000) for 5091 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 39: After refmac, R = 0.2117 (Rfree = 0.000) for 5074 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 5066 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 3.72 Search for helices and strands: 0 residues in 0 chains, 5219 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5232 seeds are put forward Round 1: 209 peptides, 45 chains. Longest chain 9 peptides. Score 0.240 Round 2: 223 peptides, 44 chains. Longest chain 10 peptides. Score 0.282 Round 3: 225 peptides, 43 chains. Longest chain 10 peptides. Score 0.296 Round 4: 246 peptides, 49 chains. Longest chain 9 peptides. Score 0.286 Round 5: 234 peptides, 41 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 5 Chains 41, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6907 reflections ( 98.46 % complete ) and 12443 restraints for refining 5157 atoms. 11712 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2517 (Rfree = 0.000) for 5157 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 42: After refmac, R = 0.2175 (Rfree = 0.000) for 5126 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 43: After refmac, R = 0.2096 (Rfree = 0.000) for 5101 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 44: After refmac, R = 0.2137 (Rfree = 0.000) for 5076 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 45: After refmac, R = 0.1893 (Rfree = 0.000) for 5073 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 5193 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5208 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 7 peptides. Score 0.214 Round 2: 193 peptides, 37 chains. Longest chain 8 peptides. Score 0.283 Round 3: 232 peptides, 43 chains. Longest chain 11 peptides. Score 0.312 Round 4: 216 peptides, 37 chains. Longest chain 14 peptides. Score 0.335 Round 5: 222 peptides, 40 chains. Longest chain 11 peptides. Score 0.319 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 179, 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 2fna-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6907 reflections ( 98.46 % complete ) and 12246 restraints for refining 5090 atoms. 11567 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2363 (Rfree = 0.000) for 5090 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 5043 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1693 (Rfree = 0.000) for 5018 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1541 (Rfree = 0.000) for 4990 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:17:10 GMT 2018 Job finished. TimeTaking 49.61 Used memory is bytes: 18564128