Mon 24 Dec 00:44:50 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 1z85-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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/1z85-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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 00:44:54 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/1z85-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.6432 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-3.6-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: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.70 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: 65.199 3.600 Wilson plot Bfac: 73.41 7071 reflections ( 99.73 % complete ) and 0 restraints for refining 4155 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3274 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3367 (Rfree = 0.000) for 4155 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 4215 seeds are put forward NCS extension: 0 residues added, 4215 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 12 peptides. Score 0.379 Round 2: 268 peptides, 35 chains. Longest chain 18 peptides. Score 0.542 Round 3: 274 peptides, 34 chains. Longest chain 24 peptides. Score 0.566 Round 4: 275 peptides, 36 chains. Longest chain 17 peptides. Score 0.548 Round 5: 285 peptides, 30 chains. Longest chain 31 peptides. Score 0.629 Taking the results from Round 5 Chains 30, Residues 255, Estimated correctness of the model 25.6 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 6910 restraints for refining 3393 atoms. 5660 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3000 (Rfree = 0.000) for 3393 atoms. Found 21 (21 requested) and removed 41 (10 requested) atoms. Cycle 2: After refmac, R = 0.2806 (Rfree = 0.000) for 3316 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 3: After refmac, R = 0.2648 (Rfree = 0.000) for 3280 atoms. Found 17 (21 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2766 (Rfree = 0.000) for 3268 atoms. Found 18 (21 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2346 (Rfree = 0.000) for 3246 atoms. Found 9 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 3329 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3351 seeds are put forward Round 1: 267 peptides, 35 chains. Longest chain 17 peptides. Score 0.540 Round 2: 296 peptides, 32 chains. Longest chain 32 peptides. Score 0.632 Round 3: 308 peptides, 32 chains. Longest chain 35 peptides. Score 0.655 Round 4: 316 peptides, 34 chains. Longest chain 37 peptides. Score 0.652 Round 5: 296 peptides, 36 chains. Longest chain 31 peptides. Score 0.594 Taking the results from Round 3 Chains 33, Residues 276, Estimated correctness of the model 34.9 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7108 restraints for refining 3390 atoms. 5943 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2607 (Rfree = 0.000) for 3390 atoms. Found 16 (21 requested) and removed 37 (10 requested) atoms. Cycle 7: After refmac, R = 0.2559 (Rfree = 0.000) for 3340 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 8: After refmac, R = 0.2520 (Rfree = 0.000) for 3319 atoms. Found 20 (21 requested) and removed 24 (10 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 3302 atoms. Found 15 (21 requested) and removed 19 (10 requested) atoms. Cycle 10: After refmac, R = 0.2488 (Rfree = 0.000) for 3289 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 3451 seeds are put forward Round 1: 230 peptides, 32 chains. Longest chain 17 peptides. Score 0.483 Round 2: 272 peptides, 30 chains. Longest chain 31 peptides. Score 0.602 Round 3: 280 peptides, 28 chains. Longest chain 24 peptides. Score 0.637 Round 4: 263 peptides, 27 chains. Longest chain 26 peptides. Score 0.613 Round 5: 282 peptides, 30 chains. Longest chain 37 peptides. Score 0.623 Taking the results from Round 3 Chains 28, Residues 252, Estimated correctness of the model 28.5 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 6804 restraints for refining 3394 atoms. 5590 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2451 (Rfree = 0.000) for 3394 atoms. Found 17 (21 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.2468 (Rfree = 0.000) for 3343 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 13: After refmac, R = 0.2394 (Rfree = 0.000) for 3331 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 14: After refmac, R = 0.2290 (Rfree = 0.000) for 3322 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2376 (Rfree = 0.000) for 3301 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 3437 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 3462 seeds are put forward Round 1: 249 peptides, 38 chains. Longest chain 17 peptides. Score 0.463 Round 2: 265 peptides, 33 chains. Longest chain 36 peptides. Score 0.556 Round 3: 281 peptides, 32 chains. Longest chain 33 peptides. Score 0.601 Round 4: 285 peptides, 33 chains. Longest chain 23 peptides. Score 0.600 Round 5: 281 peptides, 31 chains. Longest chain 21 peptides. Score 0.611 Taking the results from Round 5 Chains 34, Residues 250, Estimated correctness of the model 18.9 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7053 restraints for refining 3394 atoms. 5932 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2786 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 17: After refmac, R = 0.2603 (Rfree = 0.000) for 3357 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 18: After refmac, R = 0.2312 (Rfree = 0.000) for 3345 atoms. Found 16 (21 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.2255 (Rfree = 0.000) for 3334 atoms. Found 9 (21 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.2447 (Rfree = 0.000) for 3317 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 3419 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3453 seeds are put forward Round 1: 243 peptides, 39 chains. Longest chain 22 peptides. Score 0.435 Round 2: 251 peptides, 31 chains. Longest chain 27 peptides. Score 0.545 Round 3: 264 peptides, 33 chains. Longest chain 40 peptides. Score 0.554 Round 4: 275 peptides, 35 chains. Longest chain 40 peptides. Score 0.558 Round 5: 271 peptides, 33 chains. Longest chain 24 peptides. Score 0.570 Taking the results from Round 5 Chains 33, Residues 238, Estimated correctness of the model 2.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7639 restraints for refining 3394 atoms. 6720 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2784 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 22: After refmac, R = 0.2616 (Rfree = 0.000) for 3367 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2615 (Rfree = 0.000) for 3356 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 24: After refmac, R = 0.2159 (Rfree = 0.000) for 3343 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 25: After refmac, R = 0.2189 (Rfree = 0.000) for 3327 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 3401 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3417 seeds are put forward Round 1: 229 peptides, 42 chains. Longest chain 18 peptides. Score 0.360 Round 2: 246 peptides, 36 chains. Longest chain 27 peptides. Score 0.478 Round 3: 265 peptides, 39 chains. Longest chain 24 peptides. Score 0.492 Round 4: 266 peptides, 35 chains. Longest chain 20 peptides. Score 0.538 Round 5: 261 peptides, 32 chains. Longest chain 26 peptides. Score 0.558 Taking the results from Round 5 Chains 34, Residues 229, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7546 restraints for refining 3393 atoms. 6630 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2625 (Rfree = 0.000) for 3393 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 27: After refmac, R = 0.2557 (Rfree = 0.000) for 3379 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 28: After refmac, R = 0.2498 (Rfree = 0.000) for 3369 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2422 (Rfree = 0.000) for 3354 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.2404 (Rfree = 0.000) for 3344 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 3466 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3482 seeds are put forward Round 1: 198 peptides, 35 chains. Longest chain 13 peptides. Score 0.358 Round 2: 235 peptides, 34 chains. Longest chain 16 peptides. Score 0.473 Round 3: 245 peptides, 35 chains. Longest chain 18 peptides. Score 0.487 Round 4: 259 peptides, 36 chains. Longest chain 20 peptides. Score 0.510 Round 5: 256 peptides, 34 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 5 Chains 35, Residues 222, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7504 restraints for refining 3394 atoms. 6622 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2549 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2566 (Rfree = 0.000) for 3375 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 33: After refmac, R = 0.2554 (Rfree = 0.000) for 3356 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 34: After refmac, R = 0.2569 (Rfree = 0.000) for 3341 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 35: After refmac, R = 0.2536 (Rfree = 0.000) for 3334 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 3483 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3501 seeds are put forward Round 1: 227 peptides, 43 chains. Longest chain 11 peptides. Score 0.342 Round 2: 259 peptides, 43 chains. Longest chain 13 peptides. Score 0.432 Round 3: 255 peptides, 39 chains. Longest chain 18 peptides. Score 0.467 Round 4: 266 peptides, 35 chains. Longest chain 22 peptides. Score 0.538 Round 5: 268 peptides, 37 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 4 Chains 35, Residues 231, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7284 restraints for refining 3394 atoms. 6315 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2461 (Rfree = 0.000) for 3394 atoms. Found 18 (21 requested) and removed 18 (10 requested) atoms. Cycle 37: After refmac, R = 0.2565 (Rfree = 0.000) for 3383 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 38: After refmac, R = 0.2419 (Rfree = 0.000) for 3376 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.2075 (Rfree = 0.000) for 3371 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2336 (Rfree = 0.000) for 3357 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 3448 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 3494 seeds are put forward Round 1: 205 peptides, 41 chains. Longest chain 13 peptides. Score 0.301 Round 2: 234 peptides, 37 chains. Longest chain 22 peptides. Score 0.435 Round 3: 237 peptides, 38 chains. Longest chain 22 peptides. Score 0.431 Round 4: 254 peptides, 39 chains. Longest chain 18 peptides. Score 0.464 Round 5: 243 peptides, 31 chains. Longest chain 24 peptides. Score 0.526 Taking the results from Round 5 Chains 31, Residues 212, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7302 restraints for refining 3394 atoms. 6377 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2594 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 42: After refmac, R = 0.2438 (Rfree = 0.000) for 3368 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 43: After refmac, R = 0.2123 (Rfree = 0.000) for 3357 atoms. Found 16 (21 requested) and removed 15 (10 requested) atoms. Cycle 44: After refmac, R = 0.2007 (Rfree = 0.000) for 3342 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.2327 (Rfree = 0.000) for 3330 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 3426 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3460 seeds are put forward Round 1: 181 peptides, 34 chains. Longest chain 12 peptides. Score 0.319 Round 2: 208 peptides, 34 chains. Longest chain 17 peptides. Score 0.399 Round 3: 195 peptides, 30 chains. Longest chain 18 peptides. Score 0.413 Round 4: 210 peptides, 31 chains. Longest chain 18 peptides. Score 0.442 Round 5: 210 peptides, 31 chains. Longest chain 17 peptides. Score 0.442 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, 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 1z85-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7071 reflections ( 99.73 % complete ) and 7729 restraints for refining 3394 atoms. 7044 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2715 (Rfree = 0.000) for 3394 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2703 (Rfree = 0.000) for 3355 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2243 (Rfree = 0.000) for 3335 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2350 (Rfree = 0.000) for 3318 atoms. TimeTaking 42.63