Sun 23 Dec 23:53:16 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 2fg0-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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/2fg0-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 23:53:20 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/2fg0-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 493 and 0 Target number of residues in the AU: 493 Target solvent content: 0.6493 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: 2fg0-3.8-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: 2fg0-3.8-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 3.800 Wilson plot Bfac: 77.32 7991 reflections ( 99.65 % complete ) and 0 restraints for refining 4371 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3083 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3112 (Rfree = 0.000) for 4371 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 4460 seeds are put forward NCS extension: 0 residues added, 4460 seeds are put forward Round 1: 261 peptides, 37 chains. Longest chain 22 peptides. Score 0.445 Round 2: 308 peptides, 28 chains. Longest chain 34 peptides. Score 0.609 Round 3: 319 peptides, 25 chains. Longest chain 40 peptides. Score 0.648 Round 4: 329 peptides, 31 chains. Longest chain 41 peptides. Score 0.619 Round 5: 310 peptides, 26 chains. Longest chain 43 peptides. Score 0.627 Taking the results from Round 3 Chains 26, Residues 294, Estimated correctness of the model 20.0 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7231 restraints for refining 3560 atoms. 5846 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2793 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 48 (9 requested) atoms. Cycle 2: After refmac, R = 0.2570 (Rfree = 0.000) for 3440 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 3: After refmac, R = 0.2577 (Rfree = 0.000) for 3421 atoms. Found 16 (18 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.2369 (Rfree = 0.000) for 3404 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2393 (Rfree = 0.000) for 3388 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3502 seeds are put forward NCS extension: 24 residues added (19 deleted due to clashes), 3526 seeds are put forward Round 1: 297 peptides, 36 chains. Longest chain 26 peptides. Score 0.524 Round 2: 303 peptides, 31 chains. Longest chain 22 peptides. Score 0.577 Round 3: 303 peptides, 35 chains. Longest chain 20 peptides. Score 0.544 Round 4: 324 peptides, 36 chains. Longest chain 29 peptides. Score 0.572 Round 5: 315 peptides, 32 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 5 Chains 34, Residues 283, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7859 restraints for refining 3559 atoms. 6721 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2778 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 7: After refmac, R = 0.2505 (Rfree = 0.000) for 3519 atoms. Found 12 (19 requested) and removed 19 (9 requested) atoms. Cycle 8: After refmac, R = 0.2398 (Rfree = 0.000) for 3489 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2338 (Rfree = 0.000) for 3478 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.2356 (Rfree = 0.000) for 3460 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3572 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3598 seeds are put forward Round 1: 286 peptides, 37 chains. Longest chain 18 peptides. Score 0.495 Round 2: 318 peptides, 33 chains. Longest chain 31 peptides. Score 0.586 Round 3: 307 peptides, 33 chains. Longest chain 22 peptides. Score 0.567 Round 4: 310 peptides, 34 chains. Longest chain 20 peptides. Score 0.564 Round 5: 322 peptides, 26 chains. Longest chain 33 peptides. Score 0.645 Taking the results from Round 5 Chains 32, Residues 296, Estimated correctness of the model 18.7 % 6 chains (79 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 6974 restraints for refining 3560 atoms. 5548 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2585 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 12: After refmac, R = 0.2449 (Rfree = 0.000) for 3497 atoms. Found 17 (19 requested) and removed 19 (9 requested) atoms. Cycle 13: After refmac, R = 0.2389 (Rfree = 0.000) for 3477 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.2400 (Rfree = 0.000) for 3452 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2388 (Rfree = 0.000) for 3438 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3542 seeds are put forward NCS extension: 0 residues added, 3542 seeds are put forward Round 1: 291 peptides, 39 chains. Longest chain 20 peptides. Score 0.487 Round 2: 305 peptides, 36 chains. Longest chain 27 peptides. Score 0.539 Round 3: 312 peptides, 33 chains. Longest chain 26 peptides. Score 0.576 Round 4: 302 peptides, 32 chains. Longest chain 28 peptides. Score 0.567 Round 5: 308 peptides, 33 chains. Longest chain 23 peptides. Score 0.569 Taking the results from Round 3 Chains 37, Residues 279, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7532 restraints for refining 3559 atoms. 6331 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2543 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 17: After refmac, R = 0.2383 (Rfree = 0.000) for 3537 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 18: After refmac, R = 0.2289 (Rfree = 0.000) for 3517 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.2221 (Rfree = 0.000) for 3499 atoms. Found 8 (19 requested) and removed 17 (9 requested) atoms. Cycle 20: After refmac, R = 0.2184 (Rfree = 0.000) for 3486 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 3580 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3601 seeds are put forward Round 1: 285 peptides, 43 chains. Longest chain 18 peptides. Score 0.439 Round 2: 311 peptides, 36 chains. Longest chain 35 peptides. Score 0.550 Round 3: 298 peptides, 30 chains. Longest chain 27 peptides. Score 0.576 Round 4: 313 peptides, 36 chains. Longest chain 22 peptides. Score 0.553 Round 5: 319 peptides, 32 chains. Longest chain 27 peptides. Score 0.595 Taking the results from Round 5 Chains 32, Residues 287, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7717 restraints for refining 3559 atoms. 6581 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2511 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 22: After refmac, R = 0.2353 (Rfree = 0.000) for 3544 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2305 (Rfree = 0.000) for 3541 atoms. Found 7 (19 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.2277 (Rfree = 0.000) for 3528 atoms. Found 3 (19 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.2288 (Rfree = 0.000) for 3512 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3636 seeds are put forward Round 1: 263 peptides, 42 chains. Longest chain 14 peptides. Score 0.402 Round 2: 287 peptides, 36 chains. Longest chain 31 peptides. Score 0.506 Round 3: 298 peptides, 36 chains. Longest chain 25 peptides. Score 0.526 Round 4: 299 peptides, 36 chains. Longest chain 28 peptides. Score 0.528 Round 5: 305 peptides, 33 chains. Longest chain 27 peptides. Score 0.564 Taking the results from Round 5 Chains 33, Residues 272, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7787 restraints for refining 3559 atoms. 6685 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 27: After refmac, R = 0.2388 (Rfree = 0.000) for 3531 atoms. Found 12 (19 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2322 (Rfree = 0.000) for 3515 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.2278 (Rfree = 0.000) for 3504 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.2246 (Rfree = 0.000) for 3486 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3584 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 3621 seeds are put forward Round 1: 266 peptides, 43 chains. Longest chain 18 peptides. Score 0.399 Round 2: 297 peptides, 34 chains. Longest chain 38 peptides. Score 0.541 Round 3: 305 peptides, 37 chains. Longest chain 31 peptides. Score 0.531 Round 4: 287 peptides, 35 chains. Longest chain 30 peptides. Score 0.514 Round 5: 300 peptides, 34 chains. Longest chain 25 peptides. Score 0.547 Taking the results from Round 5 Chains 34, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 8015 restraints for refining 3560 atoms. 6985 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2579 (Rfree = 0.000) for 3560 atoms. Found 14 (19 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.2383 (Rfree = 0.000) for 3533 atoms. Found 16 (19 requested) and removed 25 (9 requested) atoms. Cycle 33: After refmac, R = 0.2352 (Rfree = 0.000) for 3517 atoms. Found 14 (19 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.2331 (Rfree = 0.000) for 3511 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2337 (Rfree = 0.000) for 3502 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3597 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3625 seeds are put forward Round 1: 252 peptides, 37 chains. Longest chain 18 peptides. Score 0.426 Round 2: 289 peptides, 35 chains. Longest chain 20 peptides. Score 0.518 Round 3: 290 peptides, 35 chains. Longest chain 19 peptides. Score 0.520 Round 4: 291 peptides, 34 chains. Longest chain 19 peptides. Score 0.530 Round 5: 283 peptides, 32 chains. Longest chain 21 peptides. Score 0.533 Taking the results from Round 5 Chains 33, Residues 251, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7854 restraints for refining 3559 atoms. 6828 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2587 (Rfree = 0.000) for 3559 atoms. Found 18 (19 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.2362 (Rfree = 0.000) for 3521 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2323 (Rfree = 0.000) for 3511 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2334 (Rfree = 0.000) for 3504 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.2258 (Rfree = 0.000) for 3500 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3642 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3657 seeds are put forward Round 1: 229 peptides, 37 chains. Longest chain 15 peptides. Score 0.376 Round 2: 262 peptides, 35 chains. Longest chain 21 peptides. Score 0.466 Round 3: 256 peptides, 34 chains. Longest chain 17 peptides. Score 0.463 Round 4: 270 peptides, 32 chains. Longest chain 20 peptides. Score 0.509 Round 5: 285 peptides, 32 chains. Longest chain 22 peptides. Score 0.537 Taking the results from Round 5 Chains 33, Residues 253, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7828 restraints for refining 3559 atoms. 6767 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2710 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 42: After refmac, R = 0.2530 (Rfree = 0.000) for 3518 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 43: After refmac, R = 0.2544 (Rfree = 0.000) for 3490 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 44: After refmac, R = 0.2173 (Rfree = 0.000) for 3474 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.2256 (Rfree = 0.000) for 3455 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 3557 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3577 seeds are put forward Round 1: 221 peptides, 37 chains. Longest chain 14 peptides. Score 0.357 Round 2: 263 peptides, 35 chains. Longest chain 20 peptides. Score 0.468 Round 3: 276 peptides, 38 chains. Longest chain 23 peptides. Score 0.466 Round 4: 279 peptides, 34 chains. Longest chain 19 peptides. Score 0.508 Round 5: 272 peptides, 35 chains. Longest chain 23 peptides. Score 0.486 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 245, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (245 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.65 % complete ) and 7742 restraints for refining 3559 atoms. 6723 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2407 (Rfree = 0.000) for 3559 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2331 (Rfree = 0.000) for 3531 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2288 (Rfree = 0.000) for 3511 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2265 (Rfree = 0.000) for 3497 atoms. TimeTaking 43.23