Sun 23 Dec 23:58:49 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 2fg0-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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/2fg0-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 ============================================================ Sun 23 Dec 23:58:54 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/2fg0-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 528 and 0 Target number of residues in the AU: 528 Target solvent content: 0.6243 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: 2fg0-3.4-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.75 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 3.400 Wilson plot Bfac: 63.58 11059 reflections ( 99.74 % complete ) and 0 restraints for refining 4379 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.2926 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3235 (Rfree = 0.000) for 4379 atoms. Found 33 (33 requested) and removed 32 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 4465 seeds are put forward NCS extension: 0 residues added, 4465 seeds are put forward Round 1: 255 peptides, 40 chains. Longest chain 14 peptides. Score 0.404 Round 2: 318 peptides, 34 chains. Longest chain 22 peptides. Score 0.578 Round 3: 329 peptides, 32 chains. Longest chain 49 peptides. Score 0.611 Round 4: 332 peptides, 30 chains. Longest chain 32 peptides. Score 0.631 Round 5: 338 peptides, 29 chains. Longest chain 36 peptides. Score 0.647 Taking the results from Round 5 Chains 36, Residues 309, Estimated correctness of the model 43.3 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7097 restraints for refining 3574 atoms. 5709 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2890 (Rfree = 0.000) for 3574 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 2: After refmac, R = 0.2808 (Rfree = 0.000) for 3452 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 3: After refmac, R = 0.2744 (Rfree = 0.000) for 3393 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2588 (Rfree = 0.000) for 3369 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 5: After refmac, R = 0.2547 (Rfree = 0.000) for 3363 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3505 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3534 seeds are put forward Round 1: 313 peptides, 39 chains. Longest chain 26 peptides. Score 0.528 Round 2: 324 peptides, 35 chains. Longest chain 24 peptides. Score 0.580 Round 3: 328 peptides, 32 chains. Longest chain 28 peptides. Score 0.610 Round 4: 348 peptides, 31 chains. Longest chain 32 peptides. Score 0.648 Round 5: 345 peptides, 33 chains. Longest chain 30 peptides. Score 0.629 Taking the results from Round 4 Chains 35, Residues 317, Estimated correctness of the model 43.6 % 7 chains (127 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6472 restraints for refining 3579 atoms. 4747 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2765 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 35 (13 requested) atoms. Cycle 7: After refmac, R = 0.2631 (Rfree = 0.000) for 3519 atoms. Found 11 (26 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2561 (Rfree = 0.000) for 3490 atoms. Found 17 (26 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.2524 (Rfree = 0.000) for 3482 atoms. Found 14 (26 requested) and removed 17 (13 requested) atoms. Cycle 10: After refmac, R = 0.2552 (Rfree = 0.000) for 3472 atoms. Found 21 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3583 seeds are put forward NCS extension: 10 residues added (15 deleted due to clashes), 3593 seeds are put forward Round 1: 329 peptides, 42 chains. Longest chain 30 peptides. Score 0.533 Round 2: 341 peptides, 33 chains. Longest chain 37 peptides. Score 0.623 Round 3: 350 peptides, 27 chains. Longest chain 46 peptides. Score 0.678 Round 4: 351 peptides, 29 chains. Longest chain 38 peptides. Score 0.666 Round 5: 345 peptides, 31 chains. Longest chain 29 peptides. Score 0.643 Taking the results from Round 3 Chains 29, Residues 323, Estimated correctness of the model 52.0 % 6 chains (156 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 5984 restraints for refining 3579 atoms. 4091 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2691 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 35 (13 requested) atoms. Cycle 12: After refmac, R = 0.2575 (Rfree = 0.000) for 3548 atoms. Found 18 (26 requested) and removed 23 (13 requested) atoms. Cycle 13: After refmac, R = 0.2612 (Rfree = 0.000) for 3533 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2568 (Rfree = 0.000) for 3530 atoms. Found 22 (26 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2551 (Rfree = 0.000) for 3522 atoms. Found 21 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3631 seeds are put forward NCS extension: 39 residues added (7 deleted due to clashes), 3670 seeds are put forward Round 1: 310 peptides, 33 chains. Longest chain 32 peptides. Score 0.572 Round 2: 335 peptides, 34 chains. Longest chain 21 peptides. Score 0.606 Round 3: 337 peptides, 33 chains. Longest chain 35 peptides. Score 0.616 Round 4: 343 peptides, 31 chains. Longest chain 37 peptides. Score 0.640 Round 5: 350 peptides, 32 chains. Longest chain 50 peptides. Score 0.643 Taking the results from Round 5 Chains 33, Residues 318, Estimated correctness of the model 42.1 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7142 restraints for refining 3579 atoms. 5703 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2716 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 17: After refmac, R = 0.2607 (Rfree = 0.000) for 3562 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 18: After refmac, R = 0.2544 (Rfree = 0.000) for 3553 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 19: After refmac, R = 0.2568 (Rfree = 0.000) for 3555 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 20: After refmac, R = 0.2462 (Rfree = 0.000) for 3546 atoms. Found 23 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3684 seeds are put forward NCS extension: 35 residues added (9 deleted due to clashes), 3719 seeds are put forward Round 1: 311 peptides, 40 chains. Longest chain 30 peptides. Score 0.516 Round 2: 324 peptides, 32 chains. Longest chain 50 peptides. Score 0.603 Round 3: 345 peptides, 34 chains. Longest chain 37 peptides. Score 0.622 Round 4: 335 peptides, 28 chains. Longest chain 51 peptides. Score 0.650 Round 5: 335 peptides, 32 chains. Longest chain 42 peptides. Score 0.621 Taking the results from Round 4 Chains 31, Residues 307, Estimated correctness of the model 44.1 % 6 chains (120 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6627 restraints for refining 3579 atoms. 4960 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2772 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 22: After refmac, R = 0.2644 (Rfree = 0.000) for 3525 atoms. Found 22 (26 requested) and removed 23 (13 requested) atoms. Cycle 23: After refmac, R = 0.2541 (Rfree = 0.000) for 3510 atoms. Found 13 (26 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2477 (Rfree = 0.000) for 3499 atoms. Found 13 (26 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2446 (Rfree = 0.000) for 3486 atoms. Found 11 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.69 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward NCS extension: 48 residues added (11 deleted due to clashes), 3627 seeds are put forward Round 1: 307 peptides, 33 chains. Longest chain 21 peptides. Score 0.567 Round 2: 328 peptides, 36 chains. Longest chain 38 peptides. Score 0.579 Round 3: 323 peptides, 37 chains. Longest chain 36 peptides. Score 0.562 Round 4: 329 peptides, 31 chains. Longest chain 36 peptides. Score 0.619 Round 5: 336 peptides, 40 chains. Longest chain 22 peptides. Score 0.561 Taking the results from Round 4 Chains 34, Residues 298, Estimated correctness of the model 34.8 % 4 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7071 restraints for refining 3578 atoms. 5641 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2737 (Rfree = 0.000) for 3578 atoms. Found 22 (27 requested) and removed 20 (13 requested) atoms. Cycle 27: After refmac, R = 0.2573 (Rfree = 0.000) for 3552 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2521 (Rfree = 0.000) for 3531 atoms. Found 8 (26 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2480 (Rfree = 0.000) for 3511 atoms. Found 15 (26 requested) and removed 22 (13 requested) atoms. Cycle 30: After refmac, R = 0.2410 (Rfree = 0.000) for 3495 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 34 residues added (10 deleted due to clashes), 3627 seeds are put forward Round 1: 303 peptides, 31 chains. Longest chain 34 peptides. Score 0.577 Round 2: 318 peptides, 30 chains. Longest chain 37 peptides. Score 0.609 Round 3: 332 peptides, 28 chains. Longest chain 54 peptides. Score 0.646 Round 4: 332 peptides, 26 chains. Longest chain 51 peptides. Score 0.660 Round 5: 324 peptides, 28 chains. Longest chain 54 peptides. Score 0.634 Taking the results from Round 4 Chains 33, Residues 306, Estimated correctness of the model 47.0 % 6 chains (125 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6492 restraints for refining 3579 atoms. 4800 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2732 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 32: After refmac, R = 0.2624 (Rfree = 0.000) for 3548 atoms. Found 26 (27 requested) and removed 21 (13 requested) atoms. Cycle 33: After refmac, R = 0.2556 (Rfree = 0.000) for 3535 atoms. Found 18 (26 requested) and removed 16 (13 requested) atoms. Cycle 34: After refmac, R = 0.2464 (Rfree = 0.000) for 3523 atoms. Found 18 (26 requested) and removed 17 (13 requested) atoms. Cycle 35: After refmac, R = 0.2442 (Rfree = 0.000) for 3521 atoms. Found 15 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3607 seeds are put forward NCS extension: 72 residues added (12 deleted due to clashes), 3679 seeds are put forward Round 1: 309 peptides, 32 chains. Longest chain 28 peptides. Score 0.579 Round 2: 332 peptides, 32 chains. Longest chain 51 peptides. Score 0.616 Round 3: 324 peptides, 34 chains. Longest chain 22 peptides. Score 0.588 Round 4: 314 peptides, 35 chains. Longest chain 33 peptides. Score 0.563 Round 5: 329 peptides, 28 chains. Longest chain 37 peptides. Score 0.641 Taking the results from Round 5 Chains 31, Residues 301, Estimated correctness of the model 41.5 % 6 chains (106 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6721 restraints for refining 3579 atoms. 5120 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2703 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 37: After refmac, R = 0.2542 (Rfree = 0.000) for 3540 atoms. Found 17 (26 requested) and removed 22 (13 requested) atoms. Cycle 38: After refmac, R = 0.2538 (Rfree = 0.000) for 3522 atoms. Found 15 (26 requested) and removed 20 (13 requested) atoms. Cycle 39: After refmac, R = 0.2368 (Rfree = 0.000) for 3507 atoms. Found 8 (26 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.2344 (Rfree = 0.000) for 3490 atoms. Found 8 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 2.69 Search for helices and strands: 0 residues in 0 chains, 3581 seeds are put forward NCS extension: 27 residues added (14 deleted due to clashes), 3608 seeds are put forward Round 1: 295 peptides, 36 chains. Longest chain 29 peptides. Score 0.521 Round 2: 316 peptides, 32 chains. Longest chain 32 peptides. Score 0.590 Round 3: 328 peptides, 32 chains. Longest chain 36 peptides. Score 0.610 Round 4: 312 peptides, 34 chains. Longest chain 36 peptides. Score 0.568 Round 5: 313 peptides, 28 chains. Longest chain 39 peptides. Score 0.617 Taking the results from Round 5 Chains 31, Residues 285, Estimated correctness of the model 34.1 % 6 chains (134 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6576 restraints for refining 3578 atoms. 4960 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2700 (Rfree = 0.000) for 3578 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 42: After refmac, R = 0.2532 (Rfree = 0.000) for 3540 atoms. Found 16 (27 requested) and removed 19 (13 requested) atoms. Cycle 43: After refmac, R = 0.2414 (Rfree = 0.000) for 3521 atoms. Found 20 (26 requested) and removed 19 (13 requested) atoms. Cycle 44: After refmac, R = 0.2273 (Rfree = 0.000) for 3515 atoms. Found 11 (26 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.2261 (Rfree = 0.000) for 3497 atoms. Found 21 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 3589 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 3623 seeds are put forward Round 1: 285 peptides, 34 chains. Longest chain 21 peptides. Score 0.519 Round 2: 319 peptides, 28 chains. Longest chain 61 peptides. Score 0.626 Round 3: 330 peptides, 31 chains. Longest chain 47 peptides. Score 0.621 Round 4: 324 peptides, 31 chains. Longest chain 35 peptides. Score 0.611 Round 5: 324 peptides, 33 chains. Longest chain 33 peptides. Score 0.596 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 291, Estimated correctness of the model 36.9 % 6 chains (118 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 71 B and 84 B 27 chains (293 residues) following loop building 5 chains (130 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11059 reflections ( 99.74 % complete ) and 6600 restraints for refining 3579 atoms. 5022 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2692 (Rfree = 0.000) for 3579 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2589 (Rfree = 0.000) for 3537 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2488 (Rfree = 0.000) for 3507 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2413 (Rfree = 0.000) for 3486 atoms. TimeTaking 45.42