Mon 24 Dec 00:03:59 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 2od6-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-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/2od6-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-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 00:04:04 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-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 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.6406 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.4-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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 3.400 Wilson plot Bfac: 72.06 7188 reflections ( 98.95 % complete ) and 0 restraints for refining 3899 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3354 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2903 (Rfree = 0.000) for 3899 atoms. Found 13 (29 requested) and removed 33 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 4003 seeds are put forward NCS extension: 0 residues added, 4003 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 12 peptides. Score 0.379 Round 2: 245 peptides, 36 chains. Longest chain 20 peptides. Score 0.513 Round 3: 265 peptides, 37 chains. Longest chain 19 peptides. Score 0.556 Round 4: 268 peptides, 34 chains. Longest chain 28 peptides. Score 0.597 Round 5: 268 peptides, 31 chains. Longest chain 32 peptides. Score 0.630 Taking the results from Round 5 Chains 33, Residues 237, Estimated correctness of the model 38.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6955 restraints for refining 3201 atoms. 5998 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2768 (Rfree = 0.000) for 3201 atoms. Found 19 (24 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2562 (Rfree = 0.000) for 3155 atoms. Found 10 (24 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2435 (Rfree = 0.000) for 3137 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 4: After refmac, R = 0.2301 (Rfree = 0.000) for 3119 atoms. Found 1 (23 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2390 (Rfree = 0.000) for 3099 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3245 seeds are put forward Round 1: 244 peptides, 37 chains. Longest chain 18 peptides. Score 0.498 Round 2: 291 peptides, 37 chains. Longest chain 24 peptides. Score 0.620 Round 3: 281 peptides, 35 chains. Longest chain 26 peptides. Score 0.618 Round 4: 291 peptides, 34 chains. Longest chain 30 peptides. Score 0.650 Round 5: 282 peptides, 33 chains. Longest chain 28 peptides. Score 0.641 Taking the results from Round 4 Chains 36, Residues 257, Estimated correctness of the model 44.1 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6504 restraints for refining 3201 atoms. 5337 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2707 (Rfree = 0.000) for 3201 atoms. Found 12 (24 requested) and removed 26 (12 requested) atoms. Cycle 7: After refmac, R = 0.2657 (Rfree = 0.000) for 3165 atoms. Found 6 (24 requested) and removed 23 (12 requested) atoms. Cycle 8: After refmac, R = 0.2471 (Rfree = 0.000) for 3136 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.2376 (Rfree = 0.000) for 3125 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2404 (Rfree = 0.000) for 3114 atoms. Found 2 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3232 seeds are put forward NCS extension: 39 residues added (11 deleted due to clashes), 3271 seeds are put forward Round 1: 256 peptides, 38 chains. Longest chain 20 peptides. Score 0.520 Round 2: 280 peptides, 31 chains. Longest chain 25 peptides. Score 0.656 Round 3: 278 peptides, 32 chains. Longest chain 20 peptides. Score 0.642 Round 4: 283 peptides, 31 chains. Longest chain 22 peptides. Score 0.663 Round 5: 287 peptides, 33 chains. Longest chain 20 peptides. Score 0.652 Taking the results from Round 4 Chains 31, Residues 252, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7090 restraints for refining 3201 atoms. 6113 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2700 (Rfree = 0.000) for 3201 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 12: After refmac, R = 0.2595 (Rfree = 0.000) for 3204 atoms. Found 3 (24 requested) and removed 19 (12 requested) atoms. Cycle 13: After refmac, R = 0.2477 (Rfree = 0.000) for 3176 atoms. Found 14 (24 requested) and removed 25 (12 requested) atoms. Cycle 14: After refmac, R = 0.2567 (Rfree = 0.000) for 3159 atoms. Found 18 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.2604 (Rfree = 0.000) for 3155 atoms. Found 9 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 3284 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3298 seeds are put forward Round 1: 251 peptides, 37 chains. Longest chain 19 peptides. Score 0.518 Round 2: 279 peptides, 35 chains. Longest chain 27 peptides. Score 0.613 Round 3: 275 peptides, 32 chains. Longest chain 22 peptides. Score 0.635 Round 4: 285 peptides, 30 chains. Longest chain 26 peptides. Score 0.677 Round 5: 268 peptides, 32 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 4 Chains 31, Residues 255, Estimated correctness of the model 51.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6664 restraints for refining 3201 atoms. 5582 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2566 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 22 (12 requested) atoms. Cycle 17: After refmac, R = 0.2761 (Rfree = 0.000) for 3184 atoms. Found 18 (24 requested) and removed 17 (12 requested) atoms. Cycle 18: After refmac, R = 0.2506 (Rfree = 0.000) for 3182 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.2458 (Rfree = 0.000) for 3174 atoms. Found 9 (23 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.2269 (Rfree = 0.000) for 3163 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 3298 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 3330 seeds are put forward Round 1: 235 peptides, 37 chains. Longest chain 18 peptides. Score 0.472 Round 2: 256 peptides, 37 chains. Longest chain 19 peptides. Score 0.532 Round 3: 278 peptides, 35 chains. Longest chain 22 peptides. Score 0.611 Round 4: 271 peptides, 35 chains. Longest chain 28 peptides. Score 0.594 Round 5: 277 peptides, 38 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 3 Chains 35, Residues 243, Estimated correctness of the model 32.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7081 restraints for refining 3200 atoms. 6144 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2470 (Rfree = 0.000) for 3200 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 3188 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.2351 (Rfree = 0.000) for 3179 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2330 (Rfree = 0.000) for 3171 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2318 (Rfree = 0.000) for 3162 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3246 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3265 seeds are put forward Round 1: 263 peptides, 44 chains. Longest chain 18 peptides. Score 0.465 Round 2: 278 peptides, 35 chains. Longest chain 25 peptides. Score 0.611 Round 3: 271 peptides, 37 chains. Longest chain 19 peptides. Score 0.571 Round 4: 264 peptides, 30 chains. Longest chain 20 peptides. Score 0.631 Round 5: 276 peptides, 33 chains. Longest chain 19 peptides. Score 0.627 Taking the results from Round 4 Chains 30, Residues 234, Estimated correctness of the model 38.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7163 restraints for refining 3201 atoms. 6257 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 3201 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.2317 (Rfree = 0.000) for 3189 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2252 (Rfree = 0.000) for 3179 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2235 (Rfree = 0.000) for 3169 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 3158 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3242 seeds are put forward Round 1: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.440 Round 2: 246 peptides, 33 chains. Longest chain 19 peptides. Score 0.553 Round 3: 238 peptides, 32 chains. Longest chain 18 peptides. Score 0.543 Round 4: 254 peptides, 40 chains. Longest chain 20 peptides. Score 0.489 Round 5: 269 peptides, 33 chains. Longest chain 26 peptides. Score 0.611 Taking the results from Round 5 Chains 33, Residues 236, Estimated correctness of the model 32.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7243 restraints for refining 3201 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2512 (Rfree = 0.000) for 3201 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2355 (Rfree = 0.000) for 3186 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2365 (Rfree = 0.000) for 3177 atoms. Found 11 (24 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.2398 (Rfree = 0.000) for 3167 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 35: After refmac, R = 0.2125 (Rfree = 0.000) for 3174 atoms. Found 3 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3276 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3294 seeds are put forward Round 1: 205 peptides, 39 chains. Longest chain 18 peptides. Score 0.348 Round 2: 244 peptides, 35 chains. Longest chain 18 peptides. Score 0.523 Round 3: 228 peptides, 34 chains. Longest chain 18 peptides. Score 0.490 Round 4: 235 peptides, 34 chains. Longest chain 18 peptides. Score 0.510 Round 5: 234 peptides, 30 chains. Longest chain 18 peptides. Score 0.557 Taking the results from Round 5 Chains 30, Residues 204, Estimated correctness of the model 14.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7320 restraints for refining 3201 atoms. 6534 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2460 (Rfree = 0.000) for 3201 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2291 (Rfree = 0.000) for 3193 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.2237 (Rfree = 0.000) for 3186 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2330 (Rfree = 0.000) for 3178 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.2262 (Rfree = 0.000) for 3169 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3257 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3274 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 12 peptides. Score 0.379 Round 2: 215 peptides, 33 chains. Longest chain 16 peptides. Score 0.464 Round 3: 227 peptides, 33 chains. Longest chain 15 peptides. Score 0.500 Round 4: 234 peptides, 34 chains. Longest chain 15 peptides. Score 0.507 Round 5: 235 peptides, 29 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 29, Residues 206, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7273 restraints for refining 3201 atoms. 6478 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2425 (Rfree = 0.000) for 3201 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.2323 (Rfree = 0.000) for 3191 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.2329 (Rfree = 0.000) for 3185 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.2373 (Rfree = 0.000) for 3171 atoms. Found 12 (23 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2096 (Rfree = 0.000) for 3166 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3239 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3265 seeds are put forward Round 1: 186 peptides, 34 chains. Longest chain 13 peptides. Score 0.356 Round 2: 226 peptides, 34 chains. Longest chain 23 peptides. Score 0.484 Round 3: 207 peptides, 28 chains. Longest chain 19 peptides. Score 0.506 Round 4: 205 peptides, 29 chains. Longest chain 19 peptides. Score 0.487 Round 5: 206 peptides, 31 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 28, 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 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7188 reflections ( 98.95 % complete ) and 7419 restraints for refining 3200 atoms. 6731 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2353 (Rfree = 0.000) for 3200 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2240 (Rfree = 0.000) for 3185 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2533 (Rfree = 0.000) for 3169 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2488 (Rfree = 0.000) for 3156 atoms. TimeTaking 36.08