Mon 24 Dec 00:22:06 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 2fg0-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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/2fg0-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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 ============================================================ Mon 24 Dec 00:22:10 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/2fg0-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-4.0-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.80 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: 88.311 4.000 Wilson plot Bfac: 84.34 6886 reflections ( 99.59 % complete ) and 0 restraints for refining 4358 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3120 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3357 (Rfree = 0.000) for 4358 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 4423 seeds are put forward NCS extension: 0 residues added, 4423 seeds are put forward Round 1: 236 peptides, 35 chains. Longest chain 17 peptides. Score 0.411 Round 2: 290 peptides, 26 chains. Longest chain 30 peptides. Score 0.595 Round 3: 290 peptides, 34 chains. Longest chain 22 peptides. Score 0.528 Round 4: 289 peptides, 24 chains. Longest chain 27 peptides. Score 0.610 Round 5: 288 peptides, 28 chains. Longest chain 24 peptides. Score 0.575 Taking the results from Round 4 Chains 29, Residues 265, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7702 restraints for refining 3551 atoms. 6550 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2537 (Rfree = 0.000) for 3551 atoms. Found 16 (16 requested) and removed 55 (8 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 3413 atoms. Found 12 (16 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.2417 (Rfree = 0.000) for 3348 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 4: After refmac, R = 0.2352 (Rfree = 0.000) for 3307 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 3278 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3386 seeds are put forward Round 1: 256 peptides, 35 chains. Longest chain 17 peptides. Score 0.453 Round 2: 292 peptides, 29 chains. Longest chain 27 peptides. Score 0.574 Round 3: 293 peptides, 30 chains. Longest chain 27 peptides. Score 0.568 Round 4: 313 peptides, 33 chains. Longest chain 23 peptides. Score 0.577 Round 5: 320 peptides, 32 chains. Longest chain 44 peptides. Score 0.597 Taking the results from Round 5 Chains 34, Residues 288, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7532 restraints for refining 3506 atoms. 6375 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2538 (Rfree = 0.000) for 3506 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.2573 (Rfree = 0.000) for 3409 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 8: After refmac, R = 0.2306 (Rfree = 0.000) for 3356 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2286 (Rfree = 0.000) for 3317 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 3288 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.06 Search for helices and strands: 0 residues in 0 chains, 3452 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 3500 seeds are put forward Round 1: 275 peptides, 37 chains. Longest chain 17 peptides. Score 0.473 Round 2: 299 peptides, 35 chains. Longest chain 19 peptides. Score 0.536 Round 3: 298 peptides, 30 chains. Longest chain 32 peptides. Score 0.576 Round 4: 324 peptides, 37 chains. Longest chain 22 peptides. Score 0.564 Round 5: 315 peptides, 31 chains. Longest chain 29 peptides. Score 0.597 Taking the results from Round 5 Chains 34, Residues 284, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7339 restraints for refining 3554 atoms. 6068 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2404 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 12: After refmac, R = 0.2165 (Rfree = 0.000) for 3477 atoms. Found 14 (16 requested) and removed 18 (8 requested) atoms. Cycle 13: After refmac, R = 0.2078 (Rfree = 0.000) for 3438 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2003 (Rfree = 0.000) for 3420 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 15: After refmac, R = 0.2000 (Rfree = 0.000) for 3405 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3539 seeds are put forward Round 1: 283 peptides, 40 chains. Longest chain 22 peptides. Score 0.462 Round 2: 297 peptides, 36 chains. Longest chain 21 peptides. Score 0.524 Round 3: 280 peptides, 34 chains. Longest chain 19 peptides. Score 0.510 Round 4: 279 peptides, 33 chains. Longest chain 24 peptides. Score 0.517 Round 5: 304 peptides, 30 chains. Longest chain 23 peptides. Score 0.586 Taking the results from Round 5 Chains 30, Residues 274, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7857 restraints for refining 3555 atoms. 6777 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2353 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 17: After refmac, R = 0.2422 (Rfree = 0.000) for 3517 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 3478 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.2340 (Rfree = 0.000) for 3465 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.2205 (Rfree = 0.000) for 3435 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.04 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3590 seeds are put forward Round 1: 268 peptides, 41 chains. Longest chain 20 peptides. Score 0.422 Round 2: 297 peptides, 36 chains. Longest chain 21 peptides. Score 0.524 Round 3: 293 peptides, 34 chains. Longest chain 25 peptides. Score 0.534 Round 4: 292 peptides, 34 chains. Longest chain 25 peptides. Score 0.532 Round 5: 274 peptides, 30 chains. Longest chain 31 peptides. Score 0.534 Taking the results from Round 5 Chains 33, Residues 244, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7849 restraints for refining 3555 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2515 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 3512 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.2368 (Rfree = 0.000) for 3485 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 24: After refmac, R = 0.2466 (Rfree = 0.000) for 3466 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.2375 (Rfree = 0.000) for 3448 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 3600 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3621 seeds are put forward Round 1: 230 peptides, 38 chains. Longest chain 14 peptides. Score 0.368 Round 2: 256 peptides, 37 chains. Longest chain 13 peptides. Score 0.435 Round 3: 281 peptides, 36 chains. Longest chain 19 peptides. Score 0.494 Round 4: 284 peptides, 31 chains. Longest chain 28 peptides. Score 0.543 Round 5: 278 peptides, 34 chains. Longest chain 29 peptides. Score 0.506 Taking the results from Round 4 Chains 33, Residues 253, Estimated correctness of the model 0.0 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7676 restraints for refining 3555 atoms. 6545 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2598 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2381 (Rfree = 0.000) for 3510 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.2285 (Rfree = 0.000) for 3472 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 29: After refmac, R = 0.2490 (Rfree = 0.000) for 3443 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 30: After refmac, R = 0.2244 (Rfree = 0.000) for 3417 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3555 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 3593 seeds are put forward Round 1: 248 peptides, 45 chains. Longest chain 11 peptides. Score 0.339 Round 2: 274 peptides, 43 chains. Longest chain 14 peptides. Score 0.416 Round 3: 265 peptides, 40 chains. Longest chain 17 peptides. Score 0.425 Round 4: 279 peptides, 39 chains. Longest chain 18 peptides. Score 0.463 Round 5: 282 peptides, 38 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 5 Chains 38, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 8017 restraints for refining 3554 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2726 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 32: After refmac, R = 0.2544 (Rfree = 0.000) for 3502 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.2403 (Rfree = 0.000) for 3459 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.2387 (Rfree = 0.000) for 3431 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.2282 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3603 seeds are put forward Round 1: 212 peptides, 39 chains. Longest chain 9 peptides. Score 0.315 Round 2: 254 peptides, 35 chains. Longest chain 18 peptides. Score 0.449 Round 3: 266 peptides, 38 chains. Longest chain 23 peptides. Score 0.446 Round 4: 267 peptides, 39 chains. Longest chain 20 peptides. Score 0.439 Round 5: 264 peptides, 35 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 5 Chains 35, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 8247 restraints for refining 3555 atoms. 7366 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2544 (Rfree = 0.000) for 3555 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.2488 (Rfree = 0.000) for 3528 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2435 (Rfree = 0.000) for 3504 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 39: After refmac, R = 0.2316 (Rfree = 0.000) for 3481 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.2493 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3574 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3608 seeds are put forward Round 1: 227 peptides, 42 chains. Longest chain 10 peptides. Score 0.320 Round 2: 262 peptides, 40 chains. Longest chain 11 peptides. Score 0.419 Round 3: 279 peptides, 38 chains. Longest chain 17 peptides. Score 0.472 Round 4: 279 peptides, 38 chains. Longest chain 20 peptides. Score 0.472 Round 5: 273 peptides, 38 chains. Longest chain 19 peptides. Score 0.460 Taking the results from Round 4 Chains 39, Residues 241, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7785 restraints for refining 3554 atoms. 6740 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2600 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2449 (Rfree = 0.000) for 3513 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2410 (Rfree = 0.000) for 3495 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.2220 (Rfree = 0.000) for 3489 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2257 (Rfree = 0.000) for 3489 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 3588 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3603 seeds are put forward Round 1: 204 peptides, 39 chains. Longest chain 12 peptides. Score 0.296 Round 2: 233 peptides, 33 chains. Longest chain 20 peptides. Score 0.424 Round 3: 241 peptides, 35 chains. Longest chain 14 peptides. Score 0.422 Round 4: 246 peptides, 35 chains. Longest chain 14 peptides. Score 0.433 Round 5: 255 peptides, 37 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 211, 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 2fg0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6886 reflections ( 99.59 % complete ) and 8480 restraints for refining 3554 atoms. 7671 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2541 (Rfree = 0.000) for 3554 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2338 (Rfree = 0.000) for 3514 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2295 (Rfree = 0.000) for 3491 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2508 (Rfree = 0.000) for 3467 atoms. TimeTaking 44.03