null Mon 24 Dec 07:26:11 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 2fg0-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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/2fg0-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 07:26:15 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/2fg0-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.4-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 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-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: 2fg0-3.4-parrot-noncs.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 4375 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.2938 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3095 (Rfree = 0.000) for 4375 atoms. Found 33 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.74 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: 281 peptides, 37 chains. Longest chain 22 peptides. Score 0.485 Round 2: 334 peptides, 35 chains. Longest chain 26 peptides. Score 0.597 Round 3: 342 peptides, 33 chains. Longest chain 31 peptides. Score 0.624 Round 4: 354 peptides, 32 chains. Longest chain 33 peptides. Score 0.649 Round 5: 355 peptides, 28 chains. Longest chain 51 peptides. Score 0.678 Taking the results from Round 5 Chains 33, Residues 327, Estimated correctness of the model 52.0 % 6 chains (117 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6451 restraints for refining 3578 atoms. 4712 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2741 (Rfree = 0.000) for 3578 atoms. Found 21 (27 requested) and removed 47 (13 requested) atoms. Cycle 2: After refmac, R = 0.2552 (Rfree = 0.000) for 3466 atoms. Found 21 (26 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2508 (Rfree = 0.000) for 3433 atoms. Found 12 (26 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2489 (Rfree = 0.000) for 3414 atoms. Found 11 (25 requested) and removed 19 (12 requested) atoms. Cycle 5: After refmac, R = 0.2454 (Rfree = 0.000) for 3396 atoms. Found 19 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 70 residues added (8 deleted due to clashes), 3581 seeds are put forward Round 1: 326 peptides, 33 chains. Longest chain 25 peptides. Score 0.599 Round 2: 349 peptides, 29 chains. Longest chain 41 peptides. Score 0.663 Round 3: 359 peptides, 28 chains. Longest chain 39 peptides. Score 0.684 Round 4: 346 peptides, 25 chains. Longest chain 40 peptides. Score 0.686 Round 5: 350 peptides, 27 chains. Longest chain 41 peptides. Score 0.678 Taking the results from Round 4 Chains 29, Residues 321, Estimated correctness of the model 54.2 % 5 chains (109 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6512 restraints for refining 3578 atoms. 4795 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2762 (Rfree = 0.000) for 3578 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 7: After refmac, R = 0.2668 (Rfree = 0.000) for 3543 atoms. Found 21 (26 requested) and removed 31 (13 requested) atoms. Cycle 8: After refmac, R = 0.2554 (Rfree = 0.000) for 3518 atoms. Found 21 (26 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2565 (Rfree = 0.000) for 3505 atoms. Found 13 (26 requested) and removed 27 (13 requested) atoms. Cycle 10: After refmac, R = 0.2465 (Rfree = 0.000) for 3485 atoms. Found 14 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 2.77 Search for helices and strands: 0 residues in 0 chains, 3580 seeds are put forward NCS extension: 37 residues added (15 deleted due to clashes), 3617 seeds are put forward Round 1: 338 peptides, 33 chains. Longest chain 39 peptides. Score 0.618 Round 2: 354 peptides, 31 chains. Longest chain 29 peptides. Score 0.656 Round 3: 341 peptides, 34 chains. Longest chain 29 peptides. Score 0.615 Round 4: 336 peptides, 32 chains. Longest chain 39 peptides. Score 0.622 Round 5: 345 peptides, 33 chains. Longest chain 39 peptides. Score 0.629 Taking the results from Round 2 Chains 35, Residues 323, Estimated correctness of the model 45.9 % 6 chains (100 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6683 restraints for refining 3577 atoms. 5014 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2744 (Rfree = 0.000) for 3577 atoms. Found 20 (27 requested) and removed 27 (13 requested) atoms. Cycle 12: After refmac, R = 0.2641 (Rfree = 0.000) for 3548 atoms. Found 15 (26 requested) and removed 36 (13 requested) atoms. Cycle 13: After refmac, R = 0.2566 (Rfree = 0.000) for 3523 atoms. Found 7 (26 requested) and removed 27 (13 requested) atoms. Cycle 14: After refmac, R = 0.2529 (Rfree = 0.000) for 3503 atoms. Found 4 (26 requested) and removed 22 (13 requested) atoms. Cycle 15: After refmac, R = 0.2562 (Rfree = 0.000) for 3483 atoms. Found 7 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.68 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 3597 seeds are put forward Round 1: 313 peptides, 32 chains. Longest chain 39 peptides. Score 0.585 Round 2: 332 peptides, 34 chains. Longest chain 24 peptides. Score 0.601 Round 3: 335 peptides, 33 chains. Longest chain 45 peptides. Score 0.613 Round 4: 343 peptides, 35 chains. Longest chain 23 peptides. Score 0.611 Round 5: 346 peptides, 33 chains. Longest chain 31 peptides. Score 0.630 Taking the results from Round 5 Chains 34, Residues 313, Estimated correctness of the model 38.2 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6943 restraints for refining 3579 atoms. 5389 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2663 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 17: After refmac, R = 0.2488 (Rfree = 0.000) for 3540 atoms. Found 21 (27 requested) and removed 19 (13 requested) atoms. Cycle 18: After refmac, R = 0.2419 (Rfree = 0.000) for 3533 atoms. Found 13 (26 requested) and removed 17 (13 requested) atoms. Cycle 19: After refmac, R = 0.2379 (Rfree = 0.000) for 3521 atoms. Found 13 (26 requested) and removed 19 (13 requested) atoms. Cycle 20: After refmac, R = 0.2310 (Rfree = 0.000) for 3512 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 3621 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 3647 seeds are put forward Round 1: 307 peptides, 34 chains. Longest chain 23 peptides. Score 0.559 Round 2: 357 peptides, 30 chains. Longest chain 38 peptides. Score 0.667 Round 3: 342 peptides, 31 chains. Longest chain 29 peptides. Score 0.639 Round 4: 338 peptides, 34 chains. Longest chain 33 peptides. Score 0.611 Round 5: 341 peptides, 31 chains. Longest chain 40 peptides. Score 0.637 Taking the results from Round 2 Chains 38, Residues 327, Estimated correctness of the model 49.0 % 10 chains (152 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6039 restraints for refining 3579 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2783 (Rfree = 0.000) for 3579 atoms. Found 21 (27 requested) and removed 24 (13 requested) atoms. Cycle 22: After refmac, R = 0.2598 (Rfree = 0.000) for 3565 atoms. Found 19 (27 requested) and removed 37 (13 requested) atoms. Cycle 23: After refmac, R = 0.2554 (Rfree = 0.000) for 3538 atoms. Found 12 (26 requested) and removed 22 (13 requested) atoms. Cycle 24: After refmac, R = 0.2479 (Rfree = 0.000) for 3521 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.2524 (Rfree = 0.000) for 3507 atoms. Found 6 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 3631 seeds are put forward Round 1: 305 peptides, 38 chains. Longest chain 21 peptides. Score 0.522 Round 2: 337 peptides, 34 chains. Longest chain 28 peptides. Score 0.609 Round 3: 334 peptides, 30 chains. Longest chain 32 peptides. Score 0.634 Round 4: 330 peptides, 28 chains. Longest chain 32 peptides. Score 0.643 Round 5: 339 peptides, 32 chains. Longest chain 25 peptides. Score 0.627 Taking the results from Round 4 Chains 33, Residues 302, Estimated correctness of the model 42.1 % 6 chains (82 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6910 restraints for refining 3579 atoms. 5423 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2619 (Rfree = 0.000) for 3579 atoms. Found 23 (27 requested) and removed 30 (13 requested) atoms. Cycle 27: After refmac, R = 0.2507 (Rfree = 0.000) for 3547 atoms. Found 15 (26 requested) and removed 24 (13 requested) atoms. Cycle 28: After refmac, R = 0.2431 (Rfree = 0.000) for 3525 atoms. Found 10 (26 requested) and removed 21 (13 requested) atoms. Cycle 29: After refmac, R = 0.2394 (Rfree = 0.000) for 3508 atoms. Found 10 (26 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.2408 (Rfree = 0.000) for 3504 atoms. Found 11 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.72 Search for helices and strands: 0 residues in 0 chains, 3616 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3644 seeds are put forward Round 1: 320 peptides, 37 chains. Longest chain 26 peptides. Score 0.557 Round 2: 347 peptides, 33 chains. Longest chain 45 peptides. Score 0.632 Round 3: 351 peptides, 32 chains. Longest chain 44 peptides. Score 0.645 Round 4: 351 peptides, 30 chains. Longest chain 44 peptides. Score 0.659 Round 5: 357 peptides, 32 chains. Longest chain 51 peptides. Score 0.654 Taking the results from Round 4 Chains 32, Residues 321, Estimated correctness of the model 46.7 % 7 chains (152 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6161 restraints for refining 3579 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2729 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 32: After refmac, R = 0.2636 (Rfree = 0.000) for 3556 atoms. Found 12 (26 requested) and removed 20 (13 requested) atoms. Cycle 33: After refmac, R = 0.2639 (Rfree = 0.000) for 3539 atoms. Found 20 (26 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.2617 (Rfree = 0.000) for 3537 atoms. Found 16 (26 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2654 (Rfree = 0.000) for 3534 atoms. Found 21 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 3646 seeds are put forward NCS extension: 48 residues added (21 deleted due to clashes), 3694 seeds are put forward Round 1: 306 peptides, 38 chains. Longest chain 44 peptides. Score 0.524 Round 2: 331 peptides, 32 chains. Longest chain 49 peptides. Score 0.615 Round 3: 333 peptides, 34 chains. Longest chain 40 peptides. Score 0.603 Round 4: 339 peptides, 33 chains. Longest chain 35 peptides. Score 0.620 Round 5: 343 peptides, 35 chains. Longest chain 27 peptides. Score 0.611 Taking the results from Round 4 Chains 34, Residues 306, Estimated correctness of the model 35.1 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 7149 restraints for refining 3579 atoms. 5705 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2675 (Rfree = 0.000) for 3579 atoms. Found 24 (27 requested) and removed 30 (13 requested) atoms. Cycle 37: After refmac, R = 0.2551 (Rfree = 0.000) for 3552 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2478 (Rfree = 0.000) for 3544 atoms. Found 10 (26 requested) and removed 25 (13 requested) atoms. Cycle 39: After refmac, R = 0.2440 (Rfree = 0.000) for 3525 atoms. Found 19 (26 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.2405 (Rfree = 0.000) for 3520 atoms. Found 20 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.68 Search for helices and strands: 0 residues in 0 chains, 3613 seeds are put forward NCS extension: 39 residues added (7 deleted due to clashes), 3652 seeds are put forward Round 1: 299 peptides, 41 chains. Longest chain 19 peptides. Score 0.485 Round 2: 305 peptides, 34 chains. Longest chain 23 peptides. Score 0.555 Round 3: 313 peptides, 33 chains. Longest chain 30 peptides. Score 0.577 Round 4: 312 peptides, 30 chains. Longest chain 33 peptides. Score 0.600 Round 5: 317 peptides, 30 chains. Longest chain 24 peptides. Score 0.608 Taking the results from Round 5 Chains 31, Residues 287, Estimated correctness of the model 31.3 % 7 chains (102 residues) have been docked in sequence ------------------------------------------------------ 11059 reflections ( 99.74 % complete ) and 6839 restraints for refining 3579 atoms. 5312 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2724 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.2550 (Rfree = 0.000) for 3563 atoms. Found 23 (27 requested) and removed 17 (13 requested) atoms. Cycle 43: After refmac, R = 0.2441 (Rfree = 0.000) for 3553 atoms. Found 15 (26 requested) and removed 19 (13 requested) atoms. Cycle 44: After refmac, R = 0.2388 (Rfree = 0.000) for 3541 atoms. Found 12 (26 requested) and removed 17 (13 requested) atoms. Cycle 45: After refmac, R = 0.2332 (Rfree = 0.000) for 3533 atoms. Found 6 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.70 Search for helices and strands: 0 residues in 0 chains, 3624 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 3640 seeds are put forward Round 1: 311 peptides, 42 chains. Longest chain 18 peptides. Score 0.499 Round 2: 334 peptides, 31 chains. Longest chain 27 peptides. Score 0.627 Round 3: 351 peptides, 29 chains. Longest chain 39 peptides. Score 0.666 Round 4: 355 peptides, 27 chains. Longest chain 51 peptides. Score 0.685 Round 5: 358 peptides, 30 chains. Longest chain 54 peptides. Score 0.669 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 328, Estimated correctness of the model 53.9 % 6 chains (153 residues) have been docked in sequence Sequence coverage is 46 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (328 residues) following loop building 6 chains (153 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11059 reflections ( 99.74 % complete ) and 6090 restraints for refining 3579 atoms. 4193 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2752 (Rfree = 0.000) for 3579 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2716 (Rfree = 0.000) for 3540 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2625 (Rfree = 0.000) for 3510 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2540 (Rfree = 0.000) for 3492 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:11:09 GMT 2018 Job finished. TimeTaking 44.98 Used memory is bytes: 7187968