Sun 23 Dec 23:52:34 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 2opk-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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 ============================================================ Sun 23 Dec 23:52:39 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/2opk-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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 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-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-4.0-parrot-mrncs.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 3953 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3082 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3101 (Rfree = 0.000) for 3953 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 3971 seeds are put forward NCS extension: 0 residues added, 3971 seeds are put forward Round 1: 203 peptides, 34 chains. Longest chain 14 peptides. Score 0.387 Round 2: 260 peptides, 39 chains. Longest chain 24 peptides. Score 0.483 Round 3: 269 peptides, 36 chains. Longest chain 14 peptides. Score 0.538 Round 4: 290 peptides, 37 chains. Longest chain 23 peptides. Score 0.576 Round 5: 288 peptides, 32 chains. Longest chain 22 peptides. Score 0.620 Taking the results from Round 5 Chains 32, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7067 restraints for refining 3235 atoms. 6075 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2581 (Rfree = 0.000) for 3235 atoms. Found 13 (15 requested) and removed 22 (7 requested) atoms. Cycle 2: After refmac, R = 0.2346 (Rfree = 0.000) for 3172 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2239 (Rfree = 0.000) for 3145 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 4: After refmac, R = 0.2242 (Rfree = 0.000) for 3113 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2255 (Rfree = 0.000) for 3097 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 3177 seeds are put forward Round 1: 261 peptides, 44 chains. Longest chain 16 peptides. Score 0.428 Round 2: 254 peptides, 36 chains. Longest chain 19 peptides. Score 0.502 Round 3: 273 peptides, 35 chains. Longest chain 18 peptides. Score 0.558 Round 4: 288 peptides, 41 chains. Longest chain 19 peptides. Score 0.530 Round 5: 272 peptides, 34 chains. Longest chain 26 peptides. Score 0.566 Taking the results from Round 5 Chains 34, Residues 238, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7097 restraints for refining 3235 atoms. 6148 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2359 (Rfree = 0.000) for 3235 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 7: After refmac, R = 0.2366 (Rfree = 0.000) for 3196 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 8: After refmac, R = 0.2250 (Rfree = 0.000) for 3170 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 9: After refmac, R = 0.2201 (Rfree = 0.000) for 3151 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 3131 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 3194 seeds are put forward NCS extension: 33 residues added (8 deleted due to clashes), 3227 seeds are put forward Round 1: 239 peptides, 43 chains. Longest chain 10 peptides. Score 0.379 Round 2: 272 peptides, 41 chains. Longest chain 16 peptides. Score 0.491 Round 3: 286 peptides, 34 chains. Longest chain 22 peptides. Score 0.597 Round 4: 270 peptides, 37 chains. Longest chain 15 peptides. Score 0.530 Round 5: 273 peptides, 35 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 3 Chains 34, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7172 restraints for refining 3236 atoms. 6198 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2390 (Rfree = 0.000) for 3236 atoms. Found 14 (15 requested) and removed 22 (7 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 3193 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 13: After refmac, R = 0.2309 (Rfree = 0.000) for 3167 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 14: After refmac, R = 0.2163 (Rfree = 0.000) for 3149 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 15: After refmac, R = 0.2241 (Rfree = 0.000) for 3128 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 3194 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 3223 seeds are put forward Round 1: 232 peptides, 45 chains. Longest chain 10 peptides. Score 0.334 Round 2: 258 peptides, 39 chains. Longest chain 19 peptides. Score 0.478 Round 3: 264 peptides, 38 chains. Longest chain 15 peptides. Score 0.504 Round 4: 277 peptides, 37 chains. Longest chain 23 peptides. Score 0.546 Round 5: 245 peptides, 33 chains. Longest chain 22 peptides. Score 0.513 Taking the results from Round 4 Chains 37, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7203 restraints for refining 3236 atoms. 6280 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2649 (Rfree = 0.000) for 3236 atoms. Found 15 (15 requested) and removed 34 (7 requested) atoms. Cycle 17: After refmac, R = 0.2524 (Rfree = 0.000) for 3182 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 18: After refmac, R = 0.2427 (Rfree = 0.000) for 3142 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 19: After refmac, R = 0.2312 (Rfree = 0.000) for 3120 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 20: After refmac, R = 0.2391 (Rfree = 0.000) for 3103 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 3161 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3187 seeds are put forward Round 1: 208 peptides, 37 chains. Longest chain 23 peptides. Score 0.364 Round 2: 243 peptides, 34 chains. Longest chain 22 peptides. Score 0.496 Round 3: 260 peptides, 35 chains. Longest chain 19 peptides. Score 0.527 Round 4: 239 peptides, 37 chains. Longest chain 13 peptides. Score 0.451 Round 5: 241 peptides, 32 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 3 Chains 39, Residues 225, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 6921 restraints for refining 3237 atoms. 5965 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2407 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 22: After refmac, R = 0.2255 (Rfree = 0.000) for 3191 atoms. Found 14 (15 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.2226 (Rfree = 0.000) for 3171 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.1928 (Rfree = 0.000) for 3159 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1976 (Rfree = 0.000) for 3147 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3233 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 10 peptides. Score 0.334 Round 2: 247 peptides, 38 chains. Longest chain 18 peptides. Score 0.461 Round 3: 255 peptides, 41 chains. Longest chain 12 peptides. Score 0.447 Round 4: 239 peptides, 30 chains. Longest chain 18 peptides. Score 0.531 Round 5: 229 peptides, 31 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 4 Chains 31, Residues 209, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7251 restraints for refining 3237 atoms. 6355 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2401 (Rfree = 0.000) for 3237 atoms. Found 13 (15 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.2148 (Rfree = 0.000) for 3198 atoms. Found 11 (15 requested) and removed 16 (7 requested) atoms. Cycle 28: After refmac, R = 0.2035 (Rfree = 0.000) for 3171 atoms. Found 14 (15 requested) and removed 14 (7 requested) atoms. Cycle 29: After refmac, R = 0.1977 (Rfree = 0.000) for 3159 atoms. Found 14 (15 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.2017 (Rfree = 0.000) for 3152 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 3216 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3229 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 8 peptides. Score 0.284 Round 2: 227 peptides, 41 chains. Longest chain 13 peptides. Score 0.369 Round 3: 236 peptides, 36 chains. Longest chain 15 peptides. Score 0.455 Round 4: 245 peptides, 36 chains. Longest chain 19 peptides. Score 0.479 Round 5: 244 peptides, 39 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 4 Chains 38, Residues 209, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7127 restraints for refining 3237 atoms. 6240 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2420 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 32: After refmac, R = 0.2395 (Rfree = 0.000) for 3202 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.2072 (Rfree = 0.000) for 3188 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 34: After refmac, R = 0.2146 (Rfree = 0.000) for 3169 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 35: After refmac, R = 0.2005 (Rfree = 0.000) for 3157 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3222 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 11 peptides. Score 0.296 Round 2: 234 peptides, 39 chains. Longest chain 18 peptides. Score 0.414 Round 3: 235 peptides, 39 chains. Longest chain 14 peptides. Score 0.416 Round 4: 233 peptides, 39 chains. Longest chain 16 peptides. Score 0.411 Round 5: 236 peptides, 39 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 5 Chains 39, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7564 restraints for refining 3237 atoms. 6815 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2349 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2498 (Rfree = 0.000) for 3214 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.2405 (Rfree = 0.000) for 3196 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.2325 (Rfree = 0.000) for 3180 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.2191 (Rfree = 0.000) for 3173 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3250 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 9 peptides. Score 0.259 Round 2: 186 peptides, 33 chains. Longest chain 11 peptides. Score 0.350 Round 3: 205 peptides, 33 chains. Longest chain 10 peptides. Score 0.406 Round 4: 201 peptides, 32 chains. Longest chain 12 peptides. Score 0.407 Round 5: 200 peptides, 30 chains. Longest chain 21 peptides. Score 0.429 Taking the results from Round 5 Chains 30, Residues 170, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5294 reflections ( 99.47 % complete ) and 7226 restraints for refining 3206 atoms. 6542 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2437 (Rfree = 0.000) for 3206 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 42: After refmac, R = 0.2300 (Rfree = 0.000) for 3169 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 3146 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 44: After refmac, R = 0.2187 (Rfree = 0.000) for 3143 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 45: After refmac, R = 0.2309 (Rfree = 0.000) for 3134 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 3245 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 8 peptides. Score 0.252 Round 2: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.332 Round 3: 191 peptides, 31 chains. Longest chain 14 peptides. Score 0.391 Round 4: 197 peptides, 31 chains. Longest chain 15 peptides. Score 0.408 Round 5: 179 peptides, 29 chains. Longest chain 15 peptides. Score 0.381 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 166, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2opk-4_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (166 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5294 reflections ( 99.47 % complete ) and 6992 restraints for refining 3148 atoms. 6292 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2512 (Rfree = 0.000) for 3148 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2432 (Rfree = 0.000) for 3121 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2015 (Rfree = 0.000) for 3103 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1915 (Rfree = 0.000) for 3085 atoms. TimeTaking 45.62