Mon 24 Dec 07:35:47 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fg0-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-parrot-noncs ############### 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 07:35:52 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/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-parrot-noncs/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 511 and 0 Target number of residues in the AU: 511 Target solvent content: 0.6364 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: 2fg0-3.6-parrot-noncs.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: 2fg0-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 69.79 9346 reflections ( 99.70 % complete ) and 0 restraints for refining 4338 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3062 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3066 (Rfree = 0.000) for 4338 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 4418 seeds are put forward NCS extension: 0 residues added, 4418 seeds are put forward Round 1: 288 peptides, 37 chains. Longest chain 25 peptides. Score 0.499 Round 2: 331 peptides, 31 chains. Longest chain 28 peptides. Score 0.622 Round 3: 322 peptides, 32 chains. Longest chain 28 peptides. Score 0.600 Round 4: 337 peptides, 30 chains. Longest chain 31 peptides. Score 0.639 Round 5: 346 peptides, 34 chains. Longest chain 38 peptides. Score 0.623 Taking the results from Round 4 Chains 31, Residues 307, Estimated correctness of the model 29.3 % 4 chains (70 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6960 restraints for refining 3568 atoms. 5497 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2562 (Rfree = 0.000) for 3478 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2455 (Rfree = 0.000) for 3458 atoms. Found 20 (22 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2401 (Rfree = 0.000) for 3440 atoms. Found 21 (22 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2357 (Rfree = 0.000) for 3434 atoms. Found 21 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 3549 seeds are put forward NCS extension: 14 residues added (12 deleted due to clashes), 3563 seeds are put forward Round 1: 314 peptides, 37 chains. Longest chain 19 peptides. Score 0.547 Round 2: 339 peptides, 30 chains. Longest chain 28 peptides. Score 0.642 Round 3: 319 peptides, 27 chains. Longest chain 29 peptides. Score 0.633 Round 4: 333 peptides, 32 chains. Longest chain 22 peptides. Score 0.618 Round 5: 334 peptides, 30 chains. Longest chain 28 peptides. Score 0.634 Taking the results from Round 2 Chains 33, Residues 309, Estimated correctness of the model 30.3 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7148 restraints for refining 3566 atoms. 5777 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2577 (Rfree = 0.000) for 3566 atoms. Found 18 (22 requested) and removed 29 (11 requested) atoms. Cycle 7: After refmac, R = 0.2414 (Rfree = 0.000) for 3520 atoms. Found 12 (22 requested) and removed 30 (11 requested) atoms. Cycle 8: After refmac, R = 0.2474 (Rfree = 0.000) for 3485 atoms. Found 13 (22 requested) and removed 25 (11 requested) atoms. Cycle 9: After refmac, R = 0.2365 (Rfree = 0.000) for 3466 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. Cycle 10: After refmac, R = 0.2440 (Rfree = 0.000) for 3455 atoms. Found 7 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 3590 seeds are put forward Round 1: 296 peptides, 39 chains. Longest chain 20 peptides. Score 0.497 Round 2: 328 peptides, 32 chains. Longest chain 27 peptides. Score 0.610 Round 3: 324 peptides, 34 chains. Longest chain 32 peptides. Score 0.588 Round 4: 324 peptides, 31 chains. Longest chain 36 peptides. Score 0.611 Round 5: 327 peptides, 29 chains. Longest chain 27 peptides. Score 0.631 Taking the results from Round 5 Chains 34, Residues 298, Estimated correctness of the model 26.4 % 4 chains (57 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7166 restraints for refining 3566 atoms. 5778 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2670 (Rfree = 0.000) for 3566 atoms. Found 18 (22 requested) and removed 19 (11 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 3534 atoms. Found 10 (22 requested) and removed 23 (11 requested) atoms. Cycle 13: After refmac, R = 0.2271 (Rfree = 0.000) for 3516 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.2290 (Rfree = 0.000) for 3498 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.2166 (Rfree = 0.000) for 3491 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 3598 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 3619 seeds are put forward Round 1: 319 peptides, 35 chains. Longest chain 23 peptides. Score 0.572 Round 2: 329 peptides, 31 chains. Longest chain 29 peptides. Score 0.619 Round 3: 321 peptides, 34 chains. Longest chain 31 peptides. Score 0.583 Round 4: 324 peptides, 29 chains. Longest chain 34 peptides. Score 0.626 Round 5: 339 peptides, 33 chains. Longest chain 31 peptides. Score 0.620 Taking the results from Round 4 Chains 31, Residues 295, Estimated correctness of the model 24.5 % 4 chains (79 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6917 restraints for refining 3568 atoms. 5467 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2577 (Rfree = 0.000) for 3568 atoms. Found 20 (22 requested) and removed 19 (11 requested) atoms. Cycle 17: After refmac, R = 0.2359 (Rfree = 0.000) for 3534 atoms. Found 10 (22 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.2309 (Rfree = 0.000) for 3504 atoms. Found 18 (22 requested) and removed 16 (11 requested) atoms. Cycle 19: After refmac, R = 0.2305 (Rfree = 0.000) for 3493 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2211 (Rfree = 0.000) for 3493 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3588 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3614 seeds are put forward Round 1: 296 peptides, 40 chains. Longest chain 20 peptides. Score 0.488 Round 2: 319 peptides, 32 chains. Longest chain 23 peptides. Score 0.595 Round 3: 314 peptides, 29 chains. Longest chain 35 peptides. Score 0.611 Round 4: 326 peptides, 32 chains. Longest chain 40 peptides. Score 0.607 Round 5: 333 peptides, 33 chains. Longest chain 35 peptides. Score 0.610 Taking the results from Round 3 Chains 29, Residues 285, Estimated correctness of the model 18.9 % 3 chains (54 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7248 restraints for refining 3567 atoms. 5915 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2392 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 22: After refmac, R = 0.2249 (Rfree = 0.000) for 3546 atoms. Found 18 (22 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.2185 (Rfree = 0.000) for 3541 atoms. Found 15 (22 requested) and removed 16 (11 requested) atoms. Cycle 24: After refmac, R = 0.2260 (Rfree = 0.000) for 3533 atoms. Found 11 (22 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.2211 (Rfree = 0.000) for 3530 atoms. Found 13 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 3642 seeds are put forward NCS extension: 43 residues added (10 deleted due to clashes), 3685 seeds are put forward Round 1: 300 peptides, 36 chains. Longest chain 21 peptides. Score 0.530 Round 2: 317 peptides, 38 chains. Longest chain 24 peptides. Score 0.544 Round 3: 324 peptides, 34 chains. Longest chain 22 peptides. Score 0.588 Round 4: 308 peptides, 31 chains. Longest chain 28 peptides. Score 0.585 Round 5: 322 peptides, 35 chains. Longest chain 28 peptides. Score 0.577 Taking the results from Round 3 Chains 35, Residues 290, Estimated correctness of the model 9.9 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7444 restraints for refining 3568 atoms. 6177 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2505 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.2460 (Rfree = 0.000) for 3559 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 28: After refmac, R = 0.2350 (Rfree = 0.000) for 3560 atoms. Found 15 (22 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.2499 (Rfree = 0.000) for 3553 atoms. Found 17 (22 requested) and removed 19 (11 requested) atoms. Cycle 30: After refmac, R = 0.2306 (Rfree = 0.000) for 3547 atoms. Found 12 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 2.78 Search for helices and strands: 0 residues in 0 chains, 3659 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3676 seeds are put forward Round 1: 297 peptides, 44 chains. Longest chain 19 peptides. Score 0.454 Round 2: 315 peptides, 33 chains. Longest chain 29 peptides. Score 0.581 Round 3: 330 peptides, 33 chains. Longest chain 36 peptides. Score 0.605 Round 4: 310 peptides, 35 chains. Longest chain 19 peptides. Score 0.556 Round 5: 319 peptides, 30 chains. Longest chain 29 peptides. Score 0.611 Taking the results from Round 5 Chains 32, Residues 289, Estimated correctness of the model 18.9 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7669 restraints for refining 3568 atoms. 6457 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2787 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 32: After refmac, R = 0.2616 (Rfree = 0.000) for 3542 atoms. Found 21 (22 requested) and removed 25 (11 requested) atoms. Cycle 33: After refmac, R = 0.2343 (Rfree = 0.000) for 3525 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 34: After refmac, R = 0.2409 (Rfree = 0.000) for 3519 atoms. Found 14 (22 requested) and removed 18 (11 requested) atoms. Cycle 35: After refmac, R = 0.2320 (Rfree = 0.000) for 3511 atoms. Found 7 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 2.77 Search for helices and strands: 0 residues in 0 chains, 3566 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 3593 seeds are put forward Round 1: 312 peptides, 38 chains. Longest chain 28 peptides. Score 0.535 Round 2: 322 peptides, 33 chains. Longest chain 30 peptides. Score 0.592 Round 3: 313 peptides, 37 chains. Longest chain 32 peptides. Score 0.545 Round 4: 311 peptides, 35 chains. Longest chain 31 peptides. Score 0.558 Round 5: 330 peptides, 35 chains. Longest chain 26 peptides. Score 0.590 Taking the results from Round 2 Chains 36, Residues 289, Estimated correctness of the model 11.5 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7424 restraints for refining 3568 atoms. 6169 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2604 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.2513 (Rfree = 0.000) for 3557 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. Cycle 38: After refmac, R = 0.2501 (Rfree = 0.000) for 3545 atoms. Found 8 (22 requested) and removed 31 (11 requested) atoms. Cycle 39: After refmac, R = 0.2434 (Rfree = 0.000) for 3515 atoms. Found 7 (22 requested) and removed 19 (11 requested) atoms. Cycle 40: After refmac, R = 0.2591 (Rfree = 0.000) for 3498 atoms. Found 6 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 2.77 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3589 seeds are put forward Round 1: 293 peptides, 37 chains. Longest chain 26 peptides. Score 0.508 Round 2: 312 peptides, 35 chains. Longest chain 27 peptides. Score 0.560 Round 3: 298 peptides, 28 chains. Longest chain 37 peptides. Score 0.592 Round 4: 285 peptides, 31 chains. Longest chain 29 peptides. Score 0.545 Round 5: 294 peptides, 33 chains. Longest chain 35 peptides. Score 0.544 Taking the results from Round 3 Chains 31, Residues 270, Estimated correctness of the model 11.5 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7261 restraints for refining 3568 atoms. 6005 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2764 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 42: After refmac, R = 0.2586 (Rfree = 0.000) for 3544 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 43: After refmac, R = 0.2465 (Rfree = 0.000) for 3533 atoms. Found 21 (22 requested) and removed 18 (11 requested) atoms. Cycle 44: After refmac, R = 0.2408 (Rfree = 0.000) for 3528 atoms. Found 18 (22 requested) and removed 16 (11 requested) atoms. Cycle 45: After refmac, R = 0.2402 (Rfree = 0.000) for 3516 atoms. Found 16 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3609 seeds are put forward NCS extension: 18 residues added (15 deleted due to clashes), 3627 seeds are put forward Round 1: 293 peptides, 44 chains. Longest chain 23 peptides. Score 0.446 Round 2: 307 peptides, 35 chains. Longest chain 30 peptides. Score 0.551 Round 3: 315 peptides, 36 chains. Longest chain 33 peptides. Score 0.557 Round 4: 305 peptides, 35 chains. Longest chain 23 peptides. Score 0.547 Round 5: 313 peptides, 33 chains. Longest chain 34 peptides. Score 0.577 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 280, Estimated correctness of the model 5.5 % 7 chains (117 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (280 residues) following loop building 7 chains (117 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9346 reflections ( 99.70 % complete ) and 6692 restraints for refining 3567 atoms. 5165 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2647 (Rfree = 0.000) for 3567 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2585 (Rfree = 0.000) for 3541 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2499 (Rfree = 0.000) for 3511 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2346 (Rfree = 0.000) for 3492 atoms. TimeTaking 49.65