null Tue 25 Dec 19:27:55 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 2pke-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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/2pke-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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 ============================================================ Tue 25 Dec 19:28:04 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/2pke-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.8-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.800 Wilson plot Bfac: 84.18 4203 reflections ( 95.76 % complete ) and 0 restraints for refining 4427 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3066 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3042 (Rfree = 0.000) for 4427 atoms. Found 24 (24 requested) and removed 47 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 4524 seeds are put forward NCS extension: 0 residues added, 4524 seeds are put forward Round 1: 151 peptides, 29 chains. Longest chain 13 peptides. Score 0.316 Round 2: 197 peptides, 34 chains. Longest chain 10 peptides. Score 0.408 Round 3: 199 peptides, 28 chains. Longest chain 19 peptides. Score 0.502 Round 4: 205 peptides, 32 chains. Longest chain 12 peptides. Score 0.464 Round 5: 205 peptides, 29 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 8824 restraints for refining 3632 atoms. 8109 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 3632 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2362 (Rfree = 0.000) for 3572 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 3: After refmac, R = 0.2195 (Rfree = 0.000) for 3527 atoms. Found 16 (19 requested) and removed 21 (9 requested) atoms. Cycle 4: After refmac, R = 0.2252 (Rfree = 0.000) for 3495 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 5: After refmac, R = 0.2241 (Rfree = 0.000) for 3477 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 3621 seeds are put forward NCS extension: 43 residues added (0 deleted due to clashes), 3664 seeds are put forward Round 1: 130 peptides, 26 chains. Longest chain 13 peptides. Score 0.283 Round 2: 175 peptides, 31 chains. Longest chain 14 peptides. Score 0.375 Round 3: 182 peptides, 30 chains. Longest chain 12 peptides. Score 0.416 Round 4: 188 peptides, 30 chains. Longest chain 17 peptides. Score 0.436 Round 5: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 4 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7596 restraints for refining 3327 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2118 (Rfree = 0.000) for 3327 atoms. Found 17 (18 requested) and removed 28 (9 requested) atoms. Cycle 7: After refmac, R = 0.2117 (Rfree = 0.000) for 3290 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 8: After refmac, R = 0.2001 (Rfree = 0.000) for 3279 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.1994 (Rfree = 0.000) for 3265 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 10: After refmac, R = 0.1963 (Rfree = 0.000) for 3254 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 3413 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3428 seeds are put forward Round 1: 163 peptides, 32 chains. Longest chain 9 peptides. Score 0.313 Round 2: 176 peptides, 31 chains. Longest chain 14 peptides. Score 0.378 Round 3: 190 peptides, 31 chains. Longest chain 14 peptides. Score 0.428 Round 4: 198 peptides, 32 chains. Longest chain 15 peptides. Score 0.441 Round 5: 193 peptides, 30 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7913 restraints for refining 3333 atoms. 7253 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1981 (Rfree = 0.000) for 3333 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 12: After refmac, R = 0.1991 (Rfree = 0.000) for 3313 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.1940 (Rfree = 0.000) for 3297 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 14: After refmac, R = 0.2176 (Rfree = 0.000) for 3275 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 3267 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 4.07 Search for helices and strands: 0 residues in 0 chains, 3466 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3479 seeds are put forward Round 1: 142 peptides, 29 chains. Longest chain 13 peptides. Score 0.280 Round 2: 162 peptides, 32 chains. Longest chain 16 peptides. Score 0.309 Round 3: 164 peptides, 29 chains. Longest chain 13 peptides. Score 0.366 Round 4: 165 peptides, 30 chains. Longest chain 13 peptides. Score 0.353 Round 5: 163 peptides, 27 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 5 Chains 27, Residues 136, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7564 restraints for refining 3196 atoms. 7034 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2042 (Rfree = 0.000) for 3196 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 17: After refmac, R = 0.2040 (Rfree = 0.000) for 3166 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 18: After refmac, R = 0.2083 (Rfree = 0.000) for 3151 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.2101 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 20: After refmac, R = 0.1866 (Rfree = 0.000) for 3114 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 3304 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3319 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 12 peptides. Score 0.281 Round 2: 166 peptides, 31 chains. Longest chain 14 peptides. Score 0.341 Round 3: 163 peptides, 30 chains. Longest chain 14 peptides. Score 0.346 Round 4: 180 peptides, 31 chains. Longest chain 14 peptides. Score 0.393 Round 5: 187 peptides, 32 chains. Longest chain 14 peptides. Score 0.403 Taking the results from Round 5 Chains 32, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7096 restraints for refining 3088 atoms. 6508 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2593 (Rfree = 0.000) for 3088 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 3049 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1943 (Rfree = 0.000) for 3039 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.1894 (Rfree = 0.000) for 3040 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3235 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 13 peptides. Score 0.262 Round 2: 176 peptides, 34 chains. Longest chain 14 peptides. Score 0.331 Round 3: 171 peptides, 28 chains. Longest chain 19 peptides. Score 0.408 Round 4: 171 peptides, 31 chains. Longest chain 14 peptides. Score 0.360 Round 5: 169 peptides, 28 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 3 Chains 28, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7353 restraints for refining 3139 atoms. 6809 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1948 (Rfree = 0.000) for 3139 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 27: After refmac, R = 0.1965 (Rfree = 0.000) for 3128 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.2209 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 29: After refmac, R = 0.1966 (Rfree = 0.000) for 3122 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.1959 (Rfree = 0.000) for 3113 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 3291 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3319 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 14 peptides. Score 0.259 Round 2: 151 peptides, 28 chains. Longest chain 13 peptides. Score 0.333 Round 3: 150 peptides, 26 chains. Longest chain 13 peptides. Score 0.362 Round 4: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.388 Round 5: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 4 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7593 restraints for refining 3187 atoms. 7095 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1874 (Rfree = 0.000) for 3187 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.1972 (Rfree = 0.000) for 3175 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 3167 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 34: After refmac, R = 0.1889 (Rfree = 0.000) for 3163 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 35: After refmac, R = 0.1396 (Rfree = 0.000) for 3160 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 4.10 Search for helices and strands: 0 residues in 0 chains, 3295 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3308 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 13 peptides. Score 0.260 Round 2: 116 peptides, 20 chains. Longest chain 13 peptides. Score 0.332 Round 3: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.317 Round 4: 121 peptides, 21 chains. Longest chain 13 peptides. Score 0.334 Round 5: 132 peptides, 22 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 5 Chains 22, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7745 restraints for refining 3191 atoms. 7327 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1949 (Rfree = 0.000) for 3191 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.1936 (Rfree = 0.000) for 3185 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 38: After refmac, R = 0.2219 (Rfree = 0.000) for 3169 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 39: After refmac, R = 0.1862 (Rfree = 0.000) for 3155 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 40: After refmac, R = 0.1964 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 3292 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3313 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 9 peptides. Score 0.229 Round 2: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.267 Round 3: 110 peptides, 22 chains. Longest chain 13 peptides. Score 0.270 Round 4: 102 peptides, 19 chains. Longest chain 13 peptides. Score 0.292 Round 5: 95 peptides, 19 chains. Longest chain 13 peptides. Score 0.260 Taking the results from Round 4 Chains 19, Residues 83, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7345 restraints for refining 3058 atoms. 7016 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1791 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 42: After refmac, R = 0.2127 (Rfree = 0.000) for 3052 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.1926 (Rfree = 0.000) for 3048 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.1867 (Rfree = 0.000) for 3048 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.2068 (Rfree = 0.000) for 3048 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 4.10 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 0 residues added, 3195 seeds are put forward Round 1: 97 peptides, 22 chains. Longest chain 10 peptides. Score 0.211 Round 2: 105 peptides, 20 chains. Longest chain 12 peptides. Score 0.286 Round 3: 115 peptides, 22 chains. Longest chain 12 peptides. Score 0.291 Round 4: 126 peptides, 22 chains. Longest chain 16 peptides. Score 0.337 Round 5: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.329 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 104, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 22 chains (104 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4203 reflections ( 95.76 % complete ) and 7155 restraints for refining 3057 atoms. 6731 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1933 (Rfree = 0.000) for 3057 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2040 (Rfree = 0.000) for 3039 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2092 (Rfree = 0.000) for 3019 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1965 (Rfree = 0.000) for 3006 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:22:44 GMT 2018 Job finished. TimeTaking 54.81 Used memory is bytes: 14962808