null Mon 24 Dec 07:27:24 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 2opk-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 07:27:28 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/2opk-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 389 and 0 Target number of residues in the AU: 389 Target solvent content: 0.6294 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 4.001 Wilson plot Bfac: 66.14 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5294 reflections ( 99.47 % complete ) and 0 restraints for refining 3987 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3226 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2648 (Rfree = 0.000) for 3987 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 4008 seeds are put forward NCS extension: 0 residues added, 4008 seeds are put forward Round 1: 195 peptides, 37 chains. Longest chain 13 peptides. Score 0.324 Round 2: 273 peptides, 38 chains. Longest chain 18 peptides. Score 0.526 Round 3: 312 peptides, 36 chains. Longest chain 23 peptides. Score 0.631 Round 4: 315 peptides, 39 chains. Longest chain 22 peptides. Score 0.610 Round 5: 323 peptides, 34 chains. Longest chain 18 peptides. Score 0.670 Taking the results from Round 5 Chains 40, Residues 289, Estimated correctness of the model 16.4 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6429 restraints for refining 3236 atoms. 5172 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2611 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 2: After refmac, R = 0.2457 (Rfree = 0.000) for 3150 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 3: After refmac, R = 0.2347 (Rfree = 0.000) for 3115 atoms. Found 13 (14 requested) and removed 23 (7 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 3091 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 5: After refmac, R = 0.2201 (Rfree = 0.000) for 3075 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 3153 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3168 seeds are put forward Round 1: 249 peptides, 38 chains. Longest chain 13 peptides. Score 0.466 Round 2: 287 peptides, 35 chains. Longest chain 25 peptides. Score 0.589 Round 3: 286 peptides, 35 chains. Longest chain 24 peptides. Score 0.587 Round 4: 288 peptides, 35 chains. Longest chain 27 peptides. Score 0.591 Round 5: 288 peptides, 35 chains. Longest chain 17 peptides. Score 0.591 Taking the results from Round 5 Chains 36, Residues 253, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6994 restraints for refining 3236 atoms. 5966 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2386 (Rfree = 0.000) for 3236 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 3203 atoms. Found 7 (15 requested) and removed 17 (7 requested) atoms. Cycle 8: After refmac, R = 0.2106 (Rfree = 0.000) for 3178 atoms. Found 2 (15 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.2047 (Rfree = 0.000) for 3162 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2020 (Rfree = 0.000) for 3152 atoms. Found 1 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 9 residues added (6 deleted due to clashes), 3221 seeds are put forward Round 1: 258 peptides, 40 chains. Longest chain 15 peptides. Score 0.467 Round 2: 272 peptides, 35 chains. Longest chain 18 peptides. Score 0.556 Round 3: 269 peptides, 37 chains. Longest chain 16 peptides. Score 0.527 Round 4: 268 peptides, 33 chains. Longest chain 19 peptides. Score 0.567 Round 5: 267 peptides, 36 chains. Longest chain 17 peptides. Score 0.533 Taking the results from Round 4 Chains 34, Residues 235, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6854 restraints for refining 3236 atoms. 5805 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2633 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 12: After refmac, R = 0.2446 (Rfree = 0.000) for 3177 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 13: After refmac, R = 0.2184 (Rfree = 0.000) for 3143 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.2164 (Rfree = 0.000) for 3130 atoms. Found 4 (14 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2083 (Rfree = 0.000) for 3110 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 3154 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3174 seeds are put forward Round 1: 250 peptides, 45 chains. Longest chain 13 peptides. Score 0.386 Round 2: 288 peptides, 45 chains. Longest chain 12 peptides. Score 0.488 Round 3: 290 peptides, 43 chains. Longest chain 21 peptides. Score 0.514 Round 4: 277 peptides, 39 chains. Longest chain 16 peptides. Score 0.525 Round 5: 285 peptides, 41 chains. Longest chain 15 peptides. Score 0.523 Taking the results from Round 4 Chains 39, Residues 238, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7210 restraints for refining 3237 atoms. 6270 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.2383 (Rfree = 0.000) for 3216 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 3197 atoms. Found 9 (15 requested) and removed 17 (7 requested) atoms. Cycle 19: After refmac, R = 0.2044 (Rfree = 0.000) for 3174 atoms. Found 6 (15 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 3158 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 3204 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3219 seeds are put forward Round 1: 231 peptides, 41 chains. Longest chain 17 peptides. Score 0.381 Round 2: 261 peptides, 40 chains. Longest chain 18 peptides. Score 0.474 Round 3: 277 peptides, 40 chains. Longest chain 17 peptides. Score 0.515 Round 4: 270 peptides, 41 chains. Longest chain 19 peptides. Score 0.486 Round 5: 275 peptides, 38 chains. Longest chain 16 peptides. Score 0.531 Taking the results from Round 5 Chains 41, Residues 237, Estimated correctness of the model 0.0 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6788 restraints for refining 3237 atoms. 5725 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2585 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2451 (Rfree = 0.000) for 3219 atoms. Found 5 (15 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2383 (Rfree = 0.000) for 3206 atoms. Found 1 (15 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.2354 (Rfree = 0.000) for 3190 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.2299 (Rfree = 0.000) for 3179 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3236 seeds are put forward Round 1: 216 peptides, 40 chains. Longest chain 12 peptides. Score 0.349 Round 2: 234 peptides, 36 chains. Longest chain 13 peptides. Score 0.450 Round 3: 244 peptides, 38 chains. Longest chain 18 peptides. Score 0.453 Round 4: 250 peptides, 38 chains. Longest chain 15 peptides. Score 0.469 Round 5: 263 peptides, 36 chains. Longest chain 19 peptides. Score 0.524 Taking the results from Round 5 Chains 36, Residues 227, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7143 restraints for refining 3237 atoms. 6250 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2358 (Rfree = 0.000) for 3237 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.2233 (Rfree = 0.000) for 3195 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2139 (Rfree = 0.000) for 3168 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.2124 (Rfree = 0.000) for 3163 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.1954 (Rfree = 0.000) for 3143 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3216 seeds are put forward Round 1: 214 peptides, 41 chains. Longest chain 16 peptides. Score 0.330 Round 2: 224 peptides, 37 chains. Longest chain 14 peptides. Score 0.410 Round 3: 233 peptides, 34 chains. Longest chain 20 peptides. Score 0.471 Round 4: 246 peptides, 35 chains. Longest chain 25 peptides. Score 0.493 Round 5: 242 peptides, 33 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 5 Chains 33, Residues 209, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7198 restraints for refining 3237 atoms. 6343 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2468 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.2485 (Rfree = 0.000) for 3200 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 33: After refmac, R = 0.2247 (Rfree = 0.000) for 3179 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 34: After refmac, R = 0.2205 (Rfree = 0.000) for 3162 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 35: After refmac, R = 0.2180 (Rfree = 0.000) for 3148 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 3198 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 3219 seeds are put forward Round 1: 200 peptides, 39 chains. Longest chain 13 peptides. Score 0.313 Round 2: 224 peptides, 34 chains. Longest chain 15 peptides. Score 0.446 Round 3: 246 peptides, 33 chains. Longest chain 18 peptides. Score 0.515 Round 4: 229 peptides, 32 chains. Longest chain 18 peptides. Score 0.483 Round 5: 226 peptides, 30 chains. Longest chain 21 peptides. Score 0.499 Taking the results from Round 3 Chains 33, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7255 restraints for refining 3237 atoms. 6436 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 37: After refmac, R = 0.2256 (Rfree = 0.000) for 3206 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.2249 (Rfree = 0.000) for 3188 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.2115 (Rfree = 0.000) for 3171 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 3157 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3221 seeds are put forward Round 1: 206 peptides, 39 chains. Longest chain 12 peptides. Score 0.332 Round 2: 225 peptides, 36 chains. Longest chain 13 peptides. Score 0.425 Round 3: 231 peptides, 38 chains. Longest chain 13 peptides. Score 0.417 Round 4: 223 peptides, 32 chains. Longest chain 15 peptides. Score 0.468 Round 5: 242 peptides, 37 chains. Longest chain 13 peptides. Score 0.459 Taking the results from Round 4 Chains 32, Residues 191, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7330 restraints for refining 3237 atoms. 6554 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2577 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 42: After refmac, R = 0.2505 (Rfree = 0.000) for 3209 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 43: After refmac, R = 0.2419 (Rfree = 0.000) for 3189 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 44: After refmac, R = 0.2449 (Rfree = 0.000) for 3165 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.2406 (Rfree = 0.000) for 3157 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3241 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 9 peptides. Score 0.253 Round 2: 193 peptides, 33 chains. Longest chain 15 peptides. Score 0.371 Round 3: 214 peptides, 37 chains. Longest chain 14 peptides. Score 0.381 Round 4: 212 peptides, 36 chains. Longest chain 14 peptides. Score 0.388 Round 5: 208 peptides, 37 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 176, 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 2opk-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5294 reflections ( 99.47 % complete ) and 7491 restraints for refining 3236 atoms. 6823 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2565 (Rfree = 0.000) for 3236 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2741 (Rfree = 0.000) for 3209 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2107 (Rfree = 0.000) for 3177 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2060 (Rfree = 0.000) for 3154 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:04:50 GMT 2018 Job finished. TimeTaking 37.45 Used memory is bytes: 8955768