Mon 24 Dec 00:58:14 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 1z85-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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/1z85-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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 00:58:18 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/1z85-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6328 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: 1z85-3.4-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: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.4-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 3.400 Wilson plot Bfac: 67.74 8357 reflections ( 99.77 % complete ) and 0 restraints for refining 4174 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3201 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3360 (Rfree = 0.000) for 4174 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 4210 seeds are put forward NCS extension: 0 residues added, 4210 seeds are put forward Round 1: 204 peptides, 39 chains. Longest chain 13 peptides. Score 0.324 Round 2: 259 peptides, 33 chains. Longest chain 22 peptides. Score 0.543 Round 3: 288 peptides, 33 chains. Longest chain 21 peptides. Score 0.606 Round 4: 282 peptides, 33 chains. Longest chain 22 peptides. Score 0.594 Round 5: 289 peptides, 35 chains. Longest chain 20 peptides. Score 0.589 Taking the results from Round 3 Chains 35, Residues 255, Estimated correctness of the model 30.6 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7152 restraints for refining 3403 atoms. 6039 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2882 (Rfree = 0.000) for 3403 atoms. Found 18 (25 requested) and removed 23 (12 requested) atoms. Cycle 2: After refmac, R = 0.2804 (Rfree = 0.000) for 3314 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2690 (Rfree = 0.000) for 3276 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 4: After refmac, R = 0.2654 (Rfree = 0.000) for 3235 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 5: After refmac, R = 0.2621 (Rfree = 0.000) for 3210 atoms. Found 8 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 3269 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3295 seeds are put forward Round 1: 257 peptides, 35 chains. Longest chain 23 peptides. Score 0.516 Round 2: 289 peptides, 31 chains. Longest chain 33 peptides. Score 0.627 Round 3: 290 peptides, 29 chains. Longest chain 28 peptides. Score 0.647 Round 4: 299 peptides, 29 chains. Longest chain 35 peptides. Score 0.664 Round 5: 299 peptides, 31 chains. Longest chain 24 peptides. Score 0.647 Taking the results from Round 4 Chains 35, Residues 270, Estimated correctness of the model 48.2 % 4 chains (87 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6434 restraints for refining 3404 atoms. 5008 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 3404 atoms. Found 21 (25 requested) and removed 27 (12 requested) atoms. Cycle 7: After refmac, R = 0.2688 (Rfree = 0.000) for 3352 atoms. Found 13 (25 requested) and removed 18 (12 requested) atoms. Cycle 8: After refmac, R = 0.2646 (Rfree = 0.000) for 3321 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 9: After refmac, R = 0.2592 (Rfree = 0.000) for 3300 atoms. Found 7 (25 requested) and removed 16 (12 requested) atoms. Cycle 10: After refmac, R = 0.2816 (Rfree = 0.000) for 3280 atoms. Found 12 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 3368 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 3407 seeds are put forward Round 1: 253 peptides, 34 chains. Longest chain 20 peptides. Score 0.518 Round 2: 296 peptides, 36 chains. Longest chain 27 peptides. Score 0.594 Round 3: 292 peptides, 30 chains. Longest chain 38 peptides. Score 0.642 Round 4: 284 peptides, 30 chains. Longest chain 33 peptides. Score 0.627 Round 5: 289 peptides, 29 chains. Longest chain 34 peptides. Score 0.646 Taking the results from Round 5 Chains 29, Residues 260, Estimated correctness of the model 43.0 % 3 chains (72 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6721 restraints for refining 3404 atoms. 5386 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2795 (Rfree = 0.000) for 3404 atoms. Found 21 (25 requested) and removed 33 (12 requested) atoms. Cycle 12: After refmac, R = 0.2625 (Rfree = 0.000) for 3344 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. Cycle 13: After refmac, R = 0.2564 (Rfree = 0.000) for 3324 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.2544 (Rfree = 0.000) for 3305 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 15: After refmac, R = 0.2540 (Rfree = 0.000) for 3293 atoms. Found 2 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 3360 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 3406 seeds are put forward Round 1: 255 peptides, 38 chains. Longest chain 19 peptides. Score 0.478 Round 2: 281 peptides, 33 chains. Longest chain 20 peptides. Score 0.592 Round 3: 290 peptides, 35 chains. Longest chain 26 peptides. Score 0.591 Round 4: 282 peptides, 36 chains. Longest chain 18 peptides. Score 0.564 Round 5: 284 peptides, 29 chains. Longest chain 26 peptides. Score 0.636 Taking the results from Round 5 Chains 31, Residues 255, Estimated correctness of the model 40.0 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6989 restraints for refining 3404 atoms. 5771 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2738 (Rfree = 0.000) for 3404 atoms. Found 18 (25 requested) and removed 19 (12 requested) atoms. Cycle 17: After refmac, R = 0.2603 (Rfree = 0.000) for 3380 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2579 (Rfree = 0.000) for 3367 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. Cycle 19: After refmac, R = 0.2527 (Rfree = 0.000) for 3357 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 20: After refmac, R = 0.2469 (Rfree = 0.000) for 3347 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 3420 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3441 seeds are put forward Round 1: 269 peptides, 39 chains. Longest chain 18 peptides. Score 0.502 Round 2: 297 peptides, 36 chains. Longest chain 28 peptides. Score 0.597 Round 3: 294 peptides, 34 chains. Longest chain 26 peptides. Score 0.609 Round 4: 303 peptides, 37 chains. Longest chain 28 peptides. Score 0.600 Round 5: 298 peptides, 35 chains. Longest chain 24 peptides. Score 0.608 Taking the results from Round 3 Chains 38, Residues 260, Estimated correctness of the model 31.6 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6926 restraints for refining 3404 atoms. 5689 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2784 (Rfree = 0.000) for 3404 atoms. Found 19 (25 requested) and removed 22 (12 requested) atoms. Cycle 22: After refmac, R = 0.2646 (Rfree = 0.000) for 3392 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.2577 (Rfree = 0.000) for 3381 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2547 (Rfree = 0.000) for 3372 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2508 (Rfree = 0.000) for 3365 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 3438 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3461 seeds are put forward Round 1: 252 peptides, 32 chains. Longest chain 28 peptides. Score 0.537 Round 2: 265 peptides, 34 chains. Longest chain 20 peptides. Score 0.546 Round 3: 281 peptides, 32 chains. Longest chain 31 peptides. Score 0.601 Round 4: 267 peptides, 31 chains. Longest chain 23 peptides. Score 0.581 Round 5: 278 peptides, 31 chains. Longest chain 27 peptides. Score 0.605 Taking the results from Round 5 Chains 32, Residues 247, Estimated correctness of the model 30.3 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7138 restraints for refining 3402 atoms. 5991 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2612 (Rfree = 0.000) for 3402 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 3395 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 28: After refmac, R = 0.2397 (Rfree = 0.000) for 3388 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2350 (Rfree = 0.000) for 3378 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2322 (Rfree = 0.000) for 3366 atoms. Found 2 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 3446 seeds are put forward NCS extension: 35 residues added (7 deleted due to clashes), 3481 seeds are put forward Round 1: 261 peptides, 38 chains. Longest chain 17 peptides. Score 0.493 Round 2: 254 peptides, 31 chains. Longest chain 24 peptides. Score 0.552 Round 3: 276 peptides, 33 chains. Longest chain 28 peptides. Score 0.581 Round 4: 271 peptides, 32 chains. Longest chain 22 peptides. Score 0.580 Round 5: 272 peptides, 33 chains. Longest chain 20 peptides. Score 0.572 Taking the results from Round 3 Chains 34, Residues 243, Estimated correctness of the model 22.4 % 2 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7087 restraints for refining 3404 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2647 (Rfree = 0.000) for 3404 atoms. Found 24 (25 requested) and removed 19 (12 requested) atoms. Cycle 32: After refmac, R = 0.2515 (Rfree = 0.000) for 3393 atoms. Found 13 (25 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.2505 (Rfree = 0.000) for 3382 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2486 (Rfree = 0.000) for 3361 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2423 (Rfree = 0.000) for 3351 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 3429 seeds are put forward NCS extension: 28 residues added (8 deleted due to clashes), 3457 seeds are put forward Round 1: 223 peptides, 31 chains. Longest chain 21 peptides. Score 0.476 Round 2: 262 peptides, 31 chains. Longest chain 30 peptides. Score 0.570 Round 3: 265 peptides, 28 chains. Longest chain 28 peptides. Score 0.607 Round 4: 250 peptides, 32 chains. Longest chain 21 peptides. Score 0.532 Round 5: 248 peptides, 31 chains. Longest chain 24 peptides. Score 0.538 Taking the results from Round 3 Chains 28, Residues 237, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7820 restraints for refining 3403 atoms. 6900 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2600 (Rfree = 0.000) for 3403 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.2532 (Rfree = 0.000) for 3403 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2498 (Rfree = 0.000) for 3392 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2481 (Rfree = 0.000) for 3386 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2385 (Rfree = 0.000) for 3376 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 3440 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 3459 seeds are put forward Round 1: 228 peptides, 33 chains. Longest chain 29 peptides. Score 0.466 Round 2: 217 peptides, 30 chains. Longest chain 25 peptides. Score 0.472 Round 3: 228 peptides, 29 chains. Longest chain 19 peptides. Score 0.512 Round 4: 225 peptides, 28 chains. Longest chain 29 peptides. Score 0.516 Round 5: 247 peptides, 30 chains. Longest chain 37 peptides. Score 0.547 Taking the results from Round 5 Chains 33, Residues 217, Estimated correctness of the model 10.4 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7395 restraints for refining 3403 atoms. 6400 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2637 (Rfree = 0.000) for 3403 atoms. Found 16 (25 requested) and removed 19 (12 requested) atoms. Cycle 42: After refmac, R = 0.2570 (Rfree = 0.000) for 3390 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.2538 (Rfree = 0.000) for 3376 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2518 (Rfree = 0.000) for 3366 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.2470 (Rfree = 0.000) for 3355 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 3423 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3459 seeds are put forward Round 1: 220 peptides, 34 chains. Longest chain 21 peptides. Score 0.433 Round 2: 233 peptides, 31 chains. Longest chain 35 peptides. Score 0.502 Round 3: 225 peptides, 30 chains. Longest chain 24 peptides. Score 0.493 Round 4: 220 peptides, 31 chains. Longest chain 22 peptides. Score 0.468 Round 5: 249 peptides, 35 chains. Longest chain 24 peptides. Score 0.497 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 202, Estimated correctness of the model 0.0 % 1 chains (34 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1z85-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8357 reflections ( 99.77 % complete ) and 7620 restraints for refining 3403 atoms. 6693 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2534 (Rfree = 0.000) for 3403 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2446 (Rfree = 0.000) for 3384 atoms. Found 0 (25 requested) and removed 10 (12 requested) atoms. Cycle 48: After refmac, R = 0.2436 (Rfree = 0.000) for 3371 atoms. Found 0 (25 requested) and removed 4 (12 requested) atoms. Cycle 49: After refmac, R = 0.2459 (Rfree = 0.000) for 3365 atoms. TimeTaking 40.37