null Mon 24 Dec 07:30:24 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 2otm-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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/2otm-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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 07:30:28 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/2otm-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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 359 and 0 Target number of residues in the AU: 359 Target solvent content: 0.6489 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-4.0-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.75 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: 78.536 4.001 Wilson plot Bfac: 77.35 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4718 reflections ( 99.68 % complete ) and 0 restraints for refining 4088 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2645 (Rfree = 0.000) for 4088 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.38 Search for helices and strands: 0 residues in 0 chains, 4147 seeds are put forward NCS extension: 0 residues added, 4147 seeds are put forward Round 1: 191 peptides, 30 chains. Longest chain 13 peptides. Score 0.408 Round 2: 233 peptides, 36 chains. Longest chain 14 peptides. Score 0.452 Round 3: 253 peptides, 32 chains. Longest chain 18 peptides. Score 0.549 Round 4: 244 peptides, 31 chains. Longest chain 14 peptides. Score 0.539 Round 5: 257 peptides, 32 chains. Longest chain 22 peptides. Score 0.559 Taking the results from Round 5 Chains 32, Residues 225, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7435 restraints for refining 3337 atoms. 6455 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2400 (Rfree = 0.000) for 3337 atoms. Found 10 (15 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2233 (Rfree = 0.000) for 3280 atoms. Found 2 (15 requested) and removed 15 (7 requested) atoms. Cycle 3: After refmac, R = 0.2099 (Rfree = 0.000) for 3244 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.1980 (Rfree = 0.000) for 3217 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2135 (Rfree = 0.000) for 3200 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3293 seeds are put forward Round 1: 232 peptides, 36 chains. Longest chain 13 peptides. Score 0.449 Round 2: 259 peptides, 34 chains. Longest chain 20 peptides. Score 0.542 Round 3: 262 peptides, 33 chains. Longest chain 21 peptides. Score 0.560 Round 4: 263 peptides, 34 chains. Longest chain 17 peptides. Score 0.552 Round 5: 258 peptides, 30 chains. Longest chain 19 peptides. Score 0.582 Taking the results from Round 5 Chains 30, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7576 restraints for refining 3337 atoms. 6694 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2403 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 7: After refmac, R = 0.2188 (Rfree = 0.000) for 3302 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 8: After refmac, R = 0.2162 (Rfree = 0.000) for 3282 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2097 (Rfree = 0.000) for 3270 atoms. Found 1 (15 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 3254 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 3321 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3349 seeds are put forward Round 1: 228 peptides, 42 chains. Longest chain 13 peptides. Score 0.363 Round 2: 234 peptides, 35 chains. Longest chain 14 peptides. Score 0.467 Round 3: 246 peptides, 33 chains. Longest chain 17 peptides. Score 0.521 Round 4: 252 peptides, 34 chains. Longest chain 20 peptides. Score 0.525 Round 5: 245 peptides, 33 chains. Longest chain 26 peptides. Score 0.519 Taking the results from Round 4 Chains 34, Residues 218, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7709 restraints for refining 3337 atoms. 6846 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2387 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.2120 (Rfree = 0.000) for 3324 atoms. Found 12 (15 requested) and removed 26 (7 requested) atoms. Cycle 13: After refmac, R = 0.2062 (Rfree = 0.000) for 3299 atoms. Found 1 (15 requested) and removed 35 (7 requested) atoms. Cycle 14: After refmac, R = 0.2046 (Rfree = 0.000) for 3257 atoms. Found 5 (15 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.1966 (Rfree = 0.000) for 3240 atoms. Found 3 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3296 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3323 seeds are put forward Round 1: 230 peptides, 39 chains. Longest chain 23 peptides. Score 0.407 Round 2: 229 peptides, 34 chains. Longest chain 13 peptides. Score 0.465 Round 3: 235 peptides, 35 chains. Longest chain 14 peptides. Score 0.469 Round 4: 233 peptides, 35 chains. Longest chain 15 peptides. Score 0.464 Round 5: 252 peptides, 32 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 5 Chains 38, Residues 220, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 6962 restraints for refining 3338 atoms. 5909 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2361 (Rfree = 0.000) for 3338 atoms. Found 11 (15 requested) and removed 48 (7 requested) atoms. Cycle 17: After refmac, R = 0.2113 (Rfree = 0.000) for 3272 atoms. Found 7 (15 requested) and removed 41 (7 requested) atoms. Cycle 18: After refmac, R = 0.2120 (Rfree = 0.000) for 3226 atoms. Found 6 (15 requested) and removed 32 (7 requested) atoms. Cycle 19: After refmac, R = 0.2012 (Rfree = 0.000) for 3194 atoms. Found 6 (15 requested) and removed 22 (7 requested) atoms. Cycle 20: After refmac, R = 0.2039 (Rfree = 0.000) for 3163 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3242 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 8 peptides. Score 0.303 Round 2: 234 peptides, 34 chains. Longest chain 17 peptides. Score 0.479 Round 3: 244 peptides, 35 chains. Longest chain 18 peptides. Score 0.493 Round 4: 234 peptides, 34 chains. Longest chain 19 peptides. Score 0.479 Round 5: 237 peptides, 38 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 3 Chains 35, Residues 209, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7293 restraints for refining 3259 atoms. 6477 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2063 (Rfree = 0.000) for 3259 atoms. Found 9 (15 requested) and removed 27 (7 requested) atoms. Cycle 22: After refmac, R = 0.1981 (Rfree = 0.000) for 3218 atoms. Found 6 (15 requested) and removed 28 (7 requested) atoms. Cycle 23: After refmac, R = 0.1800 (Rfree = 0.000) for 3186 atoms. Found 2 (15 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1901 (Rfree = 0.000) for 3168 atoms. Found 12 (15 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.1701 (Rfree = 0.000) for 3161 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.38 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3272 seeds are put forward Round 1: 201 peptides, 41 chains. Longest chain 9 peptides. Score 0.292 Round 2: 221 peptides, 35 chains. Longest chain 14 peptides. Score 0.431 Round 3: 225 peptides, 35 chains. Longest chain 12 peptides. Score 0.442 Round 4: 237 peptides, 36 chains. Longest chain 14 peptides. Score 0.463 Round 5: 220 peptides, 32 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 5 Chains 32, Residues 188, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7722 restraints for refining 3338 atoms. 6992 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2132 (Rfree = 0.000) for 3338 atoms. Found 13 (15 requested) and removed 26 (7 requested) atoms. Cycle 27: After refmac, R = 0.2019 (Rfree = 0.000) for 3300 atoms. Found 9 (15 requested) and removed 25 (7 requested) atoms. Cycle 28: After refmac, R = 0.1696 (Rfree = 0.000) for 3275 atoms. Found 3 (15 requested) and removed 17 (7 requested) atoms. Cycle 29: After refmac, R = 0.1634 (Rfree = 0.000) for 3257 atoms. Found 2 (15 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.1591 (Rfree = 0.000) for 3241 atoms. Found 0 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 3312 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 3322 seeds are put forward Round 1: 181 peptides, 35 chains. Longest chain 12 peptides. Score 0.310 Round 2: 198 peptides, 32 chains. Longest chain 13 peptides. Score 0.402 Round 3: 189 peptides, 32 chains. Longest chain 10 peptides. Score 0.376 Round 4: 209 peptides, 37 chains. Longest chain 15 peptides. Score 0.370 Round 5: 201 peptides, 33 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 2 Chains 32, Residues 166, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7734 restraints for refining 3312 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1836 (Rfree = 0.000) for 3312 atoms. Found 6 (15 requested) and removed 34 (7 requested) atoms. Cycle 32: After refmac, R = 0.1888 (Rfree = 0.000) for 3276 atoms. Found 4 (15 requested) and removed 21 (7 requested) atoms. Cycle 33: After refmac, R = 0.1915 (Rfree = 0.000) for 3251 atoms. Found 7 (15 requested) and removed 22 (7 requested) atoms. Cycle 34: After refmac, R = 0.1645 (Rfree = 0.000) for 3228 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. Cycle 35: After refmac, R = 0.1650 (Rfree = 0.000) for 3213 atoms. Found 1 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 3289 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3307 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 10 peptides. Score 0.301 Round 2: 208 peptides, 36 chains. Longest chain 12 peptides. Score 0.380 Round 3: 207 peptides, 35 chains. Longest chain 13 peptides. Score 0.390 Round 4: 207 peptides, 33 chains. Longest chain 13 peptides. Score 0.416 Round 5: 229 peptides, 35 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Chains 36, Residues 194, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7485 restraints for refining 3336 atoms. 6692 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2051 (Rfree = 0.000) for 3336 atoms. Found 10 (15 requested) and removed 21 (7 requested) atoms. Cycle 37: After refmac, R = 0.1894 (Rfree = 0.000) for 3307 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 3295 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 3278 atoms. Found 4 (15 requested) and removed 16 (7 requested) atoms. Cycle 40: After refmac, R = 0.1712 (Rfree = 0.000) for 3262 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 3338 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3351 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 9 peptides. Score 0.288 Round 2: 188 peptides, 35 chains. Longest chain 15 peptides. Score 0.332 Round 3: 202 peptides, 34 chains. Longest chain 16 peptides. Score 0.388 Round 4: 194 peptides, 31 chains. Longest chain 10 peptides. Score 0.404 Round 5: 204 peptides, 35 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 4 Chains 31, Residues 163, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7682 restraints for refining 3338 atoms. 7039 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1912 (Rfree = 0.000) for 3338 atoms. Found 4 (15 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.1805 (Rfree = 0.000) for 3314 atoms. Found 2 (15 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.1710 (Rfree = 0.000) for 3292 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1667 (Rfree = 0.000) for 3282 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 45: After refmac, R = 0.1641 (Rfree = 0.000) for 3272 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.37 Search for helices and strands: 0 residues in 0 chains, 3337 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3343 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 9 peptides. Score 0.278 Round 2: 175 peptides, 32 chains. Longest chain 9 peptides. Score 0.332 Round 3: 186 peptides, 33 chains. Longest chain 10 peptides. Score 0.353 Round 4: 190 peptides, 34 chains. Longest chain 9 peptides. Score 0.352 Round 5: 187 peptides, 31 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 156, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2otm-4_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (156 residues) following loop building 2 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4718 reflections ( 99.68 % complete ) and 7695 restraints for refining 3338 atoms. 7050 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2036 (Rfree = 0.000) for 3338 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2077 (Rfree = 0.000) for 3325 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1977 (Rfree = 0.000) for 3315 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1706 (Rfree = 0.000) for 3306 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:08:31 GMT 2018 Job finished. TimeTaking 38.12 Used memory is bytes: 7057624