Mon 24 Dec 07:56:36 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 2fg0-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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/2fg0-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 07:56:40 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/2fg0-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 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-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: 2fg0-3.8-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 3.800 Wilson plot Bfac: 77.32 7991 reflections ( 99.65 % complete ) and 0 restraints for refining 4369 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3030 (Rfree = 0.000) for 4369 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 2.97 Search for helices and strands: 0 residues in 0 chains, 4452 seeds are put forward NCS extension: 0 residues added, 4452 seeds are put forward Round 1: 247 peptides, 35 chains. Longest chain 19 peptides. Score 0.435 Round 2: 291 peptides, 32 chains. Longest chain 24 peptides. Score 0.547 Round 3: 307 peptides, 32 chains. Longest chain 35 peptides. Score 0.575 Round 4: 332 peptides, 25 chains. Longest chain 30 peptides. Score 0.667 Round 5: 331 peptides, 27 chains. Longest chain 42 peptides. Score 0.651 Taking the results from Round 4 Chains 27, Residues 307, Estimated correctness of the model 27.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7495 restraints for refining 3558 atoms. 6229 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2583 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2323 (Rfree = 0.000) for 3477 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 3: After refmac, R = 0.2265 (Rfree = 0.000) for 3451 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 4: After refmac, R = 0.2175 (Rfree = 0.000) for 3442 atoms. Found 17 (18 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.2216 (Rfree = 0.000) for 3430 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3550 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 3583 seeds are put forward Round 1: 280 peptides, 31 chains. Longest chain 25 peptides. Score 0.536 Round 2: 295 peptides, 27 chains. Longest chain 55 peptides. Score 0.595 Round 3: 293 peptides, 26 chains. Longest chain 47 peptides. Score 0.600 Round 4: 290 peptides, 26 chains. Longest chain 30 peptides. Score 0.595 Round 5: 295 peptides, 25 chains. Longest chain 41 peptides. Score 0.611 Taking the results from Round 5 Chains 25, Residues 270, Estimated correctness of the model 3.9 % 1 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7536 restraints for refining 3560 atoms. 6324 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2465 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 7: After refmac, R = 0.2294 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 3525 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.2170 (Rfree = 0.000) for 3513 atoms. Found 14 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2153 (Rfree = 0.000) for 3505 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3625 seeds are put forward NCS extension: 28 residues added (10 deleted due to clashes), 3653 seeds are put forward Round 1: 270 peptides, 34 chains. Longest chain 25 peptides. Score 0.491 Round 2: 291 peptides, 29 chains. Longest chain 40 peptides. Score 0.572 Round 3: 305 peptides, 30 chains. Longest chain 26 peptides. Score 0.588 Round 4: 307 peptides, 29 chains. Longest chain 25 peptides. Score 0.599 Round 5: 309 peptides, 30 chains. Longest chain 33 peptides. Score 0.595 Taking the results from Round 4 Chains 32, Residues 278, Estimated correctness of the model 0.0 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7155 restraints for refining 3560 atoms. 5805 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2543 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 12: After refmac, R = 0.2370 (Rfree = 0.000) for 3520 atoms. Found 18 (19 requested) and removed 19 (9 requested) atoms. Cycle 13: After refmac, R = 0.2303 (Rfree = 0.000) for 3494 atoms. Found 10 (19 requested) and removed 19 (9 requested) atoms. Cycle 14: After refmac, R = 0.2273 (Rfree = 0.000) for 3476 atoms. Found 9 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2237 (Rfree = 0.000) for 3462 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 2.90 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 6 residues added (11 deleted due to clashes), 3571 seeds are put forward Round 1: 296 peptides, 33 chains. Longest chain 28 peptides. Score 0.548 Round 2: 307 peptides, 30 chains. Longest chain 49 peptides. Score 0.591 Round 3: 302 peptides, 30 chains. Longest chain 33 peptides. Score 0.583 Round 4: 312 peptides, 29 chains. Longest chain 34 peptides. Score 0.607 Round 5: 300 peptides, 30 chains. Longest chain 35 peptides. Score 0.580 Taking the results from Round 4 Chains 31, Residues 283, Estimated correctness of the model 2.1 % 4 chains (76 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 6998 restraints for refining 3559 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2489 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 3513 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 18: After refmac, R = 0.2285 (Rfree = 0.000) for 3508 atoms. Found 16 (19 requested) and removed 18 (9 requested) atoms. Cycle 19: After refmac, R = 0.2216 (Rfree = 0.000) for 3497 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2297 (Rfree = 0.000) for 3488 atoms. Found 3 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3566 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 3592 seeds are put forward Round 1: 275 peptides, 34 chains. Longest chain 21 peptides. Score 0.500 Round 2: 309 peptides, 36 chains. Longest chain 30 peptides. Score 0.546 Round 3: 298 peptides, 31 chains. Longest chain 22 peptides. Score 0.568 Round 4: 310 peptides, 33 chains. Longest chain 28 peptides. Score 0.572 Round 5: 297 peptides, 30 chains. Longest chain 29 peptides. Score 0.574 Taking the results from Round 5 Chains 32, Residues 267, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7747 restraints for refining 3560 atoms. 6597 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2668 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 22: After refmac, R = 0.2933 (Rfree = 0.000) for 3530 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2773 (Rfree = 0.000) for 3521 atoms. Found 11 (19 requested) and removed 17 (9 requested) atoms. Cycle 24: After refmac, R = 0.2735 (Rfree = 0.000) for 3513 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.2952 (Rfree = 0.000) for 3504 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3609 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 3631 seeds are put forward Round 1: 269 peptides, 35 chains. Longest chain 19 peptides. Score 0.480 Round 2: 299 peptides, 30 chains. Longest chain 30 peptides. Score 0.578 Round 3: 304 peptides, 32 chains. Longest chain 27 peptides. Score 0.570 Round 4: 308 peptides, 34 chains. Longest chain 23 peptides. Score 0.561 Round 5: 302 peptides, 32 chains. Longest chain 21 peptides. Score 0.567 Taking the results from Round 2 Chains 30, Residues 269, Estimated correctness of the model 0.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7489 restraints for refining 3560 atoms. 6309 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2976 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.2887 (Rfree = 0.000) for 3542 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2970 (Rfree = 0.000) for 3531 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2914 (Rfree = 0.000) for 3515 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2314 (Rfree = 0.000) for 3507 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 3603 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3627 seeds are put forward Round 1: 262 peptides, 36 chains. Longest chain 17 peptides. Score 0.456 Round 2: 284 peptides, 33 chains. Longest chain 19 peptides. Score 0.526 Round 3: 292 peptides, 32 chains. Longest chain 25 peptides. Score 0.549 Round 4: 293 peptides, 34 chains. Longest chain 17 peptides. Score 0.534 Round 5: 281 peptides, 34 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 3 Chains 35, Residues 260, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7629 restraints for refining 3560 atoms. 6505 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2979 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 32: After refmac, R = 0.2489 (Rfree = 0.000) for 3536 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2484 (Rfree = 0.000) for 3535 atoms. Found 18 (19 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.2460 (Rfree = 0.000) for 3531 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.2339 (Rfree = 0.000) for 3531 atoms. Found 13 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3624 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3643 seeds are put forward Round 1: 261 peptides, 38 chains. Longest chain 14 peptides. Score 0.436 Round 2: 279 peptides, 36 chains. Longest chain 16 peptides. Score 0.490 Round 3: 284 peptides, 36 chains. Longest chain 21 peptides. Score 0.500 Round 4: 291 peptides, 36 chains. Longest chain 19 peptides. Score 0.513 Round 5: 290 peptides, 34 chains. Longest chain 29 peptides. Score 0.528 Taking the results from Round 5 Chains 34, Residues 256, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7876 restraints for refining 3559 atoms. 6758 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3060 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 37: After refmac, R = 0.3085 (Rfree = 0.000) for 3532 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 38: After refmac, R = 0.2474 (Rfree = 0.000) for 3518 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.2420 (Rfree = 0.000) for 3508 atoms. Found 2 (19 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2423 (Rfree = 0.000) for 3493 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3621 seeds are put forward Round 1: 237 peptides, 37 chains. Longest chain 14 peptides. Score 0.394 Round 2: 258 peptides, 33 chains. Longest chain 18 peptides. Score 0.476 Round 3: 264 peptides, 33 chains. Longest chain 17 peptides. Score 0.488 Round 4: 273 peptides, 32 chains. Longest chain 16 peptides. Score 0.514 Round 5: 258 peptides, 34 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 4 Chains 32, Residues 241, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7927 restraints for refining 3560 atoms. 6922 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2740 (Rfree = 0.000) for 3560 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2635 (Rfree = 0.000) for 3518 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2754 (Rfree = 0.000) for 3499 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2770 (Rfree = 0.000) for 3489 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.2664 (Rfree = 0.000) for 3474 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3579 seeds are put forward Round 1: 217 peptides, 38 chains. Longest chain 12 peptides. Score 0.338 Round 2: 248 peptides, 35 chains. Longest chain 18 peptides. Score 0.437 Round 3: 267 peptides, 37 chains. Longest chain 21 peptides. Score 0.457 Round 4: 278 peptides, 39 chains. Longest chain 21 peptides. Score 0.461 Round 5: 268 peptides, 34 chains. Longest chain 21 peptides. Score 0.487 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 234, 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 2fg0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.65 % complete ) and 8341 restraints for refining 3558 atoms. 7439 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2589 (Rfree = 0.000) for 3558 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2480 (Rfree = 0.000) for 3537 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2427 (Rfree = 0.000) for 3519 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2368 (Rfree = 0.000) for 3507 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 41.48