Sun 23 Dec 23:45:45 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 2ajr-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.2-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/2ajr-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.2-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 23:45:50 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/2ajr-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.2-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 591 and 0 Target number of residues in the AU: 591 Target solvent content: 0.6173 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-3.2-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: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.65 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: 29.168 3.200 Wilson plot Bfac: 59.93 14494 reflections ( 99.68 % complete ) and 0 restraints for refining 5914 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3588 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3188 (Rfree = 0.000) for 5914 atoms. Found 41 (53 requested) and removed 60 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.89 Search for helices and strands: 0 residues in 0 chains, 5990 seeds are put forward NCS extension: 0 residues added, 5990 seeds are put forward Round 1: 277 peptides, 54 chains. Longest chain 11 peptides. Score 0.307 Round 2: 352 peptides, 55 chains. Longest chain 20 peptides. Score 0.447 Round 3: 377 peptides, 59 chains. Longest chain 16 peptides. Score 0.461 Round 4: 404 peptides, 54 chains. Longest chain 28 peptides. Score 0.544 Round 5: 401 peptides, 55 chains. Longest chain 20 peptides. Score 0.532 Taking the results from Round 4 Chains 55, Residues 350, Estimated correctness of the model 25.1 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10266 restraints for refining 4835 atoms. 8812 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3007 (Rfree = 0.000) for 4835 atoms. Found 36 (43 requested) and removed 41 (21 requested) atoms. Cycle 2: After refmac, R = 0.2881 (Rfree = 0.000) for 4764 atoms. Found 33 (43 requested) and removed 34 (21 requested) atoms. Cycle 3: After refmac, R = 0.2823 (Rfree = 0.000) for 4717 atoms. Found 22 (42 requested) and removed 36 (21 requested) atoms. Cycle 4: After refmac, R = 0.2690 (Rfree = 0.000) for 4678 atoms. Found 23 (42 requested) and removed 32 (21 requested) atoms. Cycle 5: After refmac, R = 0.2684 (Rfree = 0.000) for 4660 atoms. Found 23 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4807 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4832 seeds are put forward Round 1: 383 peptides, 62 chains. Longest chain 18 peptides. Score 0.448 Round 2: 408 peptides, 52 chains. Longest chain 20 peptides. Score 0.564 Round 3: 419 peptides, 56 chains. Longest chain 22 peptides. Score 0.553 Round 4: 427 peptides, 52 chains. Longest chain 30 peptides. Score 0.593 Round 5: 424 peptides, 51 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 5 Chains 51, Residues 373, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10657 restraints for refining 4834 atoms. 9216 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2841 (Rfree = 0.000) for 4834 atoms. Found 43 (43 requested) and removed 34 (21 requested) atoms. Cycle 7: After refmac, R = 0.2675 (Rfree = 0.000) for 4818 atoms. Found 14 (43 requested) and removed 35 (21 requested) atoms. Cycle 8: After refmac, R = 0.2639 (Rfree = 0.000) for 4783 atoms. Found 14 (43 requested) and removed 32 (21 requested) atoms. Cycle 9: After refmac, R = 0.2500 (Rfree = 0.000) for 4757 atoms. Found 9 (42 requested) and removed 27 (21 requested) atoms. Cycle 10: After refmac, R = 0.2454 (Rfree = 0.000) for 4732 atoms. Found 3 (42 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 4865 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4885 seeds are put forward Round 1: 372 peptides, 57 chains. Longest chain 24 peptides. Score 0.468 Round 2: 408 peptides, 57 chains. Longest chain 22 peptides. Score 0.529 Round 3: 413 peptides, 50 chains. Longest chain 28 peptides. Score 0.585 Round 4: 415 peptides, 54 chains. Longest chain 33 peptides. Score 0.561 Round 5: 425 peptides, 47 chains. Longest chain 39 peptides. Score 0.622 Taking the results from Round 5 Chains 49, Residues 378, Estimated correctness of the model 46.9 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10209 restraints for refining 4835 atoms. 8619 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2811 (Rfree = 0.000) for 4835 atoms. Found 43 (43 requested) and removed 32 (21 requested) atoms. Cycle 12: After refmac, R = 0.2785 (Rfree = 0.000) for 4833 atoms. Found 18 (43 requested) and removed 28 (21 requested) atoms. Cycle 13: After refmac, R = 0.2618 (Rfree = 0.000) for 4817 atoms. Found 34 (43 requested) and removed 29 (21 requested) atoms. Cycle 14: After refmac, R = 0.2613 (Rfree = 0.000) for 4812 atoms. Found 25 (43 requested) and removed 29 (21 requested) atoms. Cycle 15: After refmac, R = 0.2535 (Rfree = 0.000) for 4799 atoms. Found 28 (43 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4990 seeds are put forward NCS extension: 48 residues added (8 deleted due to clashes), 5038 seeds are put forward Round 1: 382 peptides, 56 chains. Longest chain 31 peptides. Score 0.493 Round 2: 398 peptides, 51 chains. Longest chain 32 peptides. Score 0.556 Round 3: 390 peptides, 50 chains. Longest chain 32 peptides. Score 0.550 Round 4: 409 peptides, 49 chains. Longest chain 23 peptides. Score 0.586 Round 5: 385 peptides, 43 chains. Longest chain 32 peptides. Score 0.592 Taking the results from Round 5 Chains 44, Residues 342, Estimated correctness of the model 38.9 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10262 restraints for refining 4835 atoms. 8761 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2750 (Rfree = 0.000) for 4835 atoms. Found 25 (43 requested) and removed 29 (21 requested) atoms. Cycle 17: After refmac, R = 0.2663 (Rfree = 0.000) for 4812 atoms. Found 18 (43 requested) and removed 28 (21 requested) atoms. Cycle 18: After refmac, R = 0.2618 (Rfree = 0.000) for 4784 atoms. Found 30 (43 requested) and removed 29 (21 requested) atoms. Cycle 19: After refmac, R = 0.2531 (Rfree = 0.000) for 4776 atoms. Found 29 (42 requested) and removed 27 (21 requested) atoms. Cycle 20: After refmac, R = 0.2498 (Rfree = 0.000) for 4770 atoms. Found 21 (42 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4921 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 4945 seeds are put forward Round 1: 375 peptides, 56 chains. Longest chain 23 peptides. Score 0.481 Round 2: 383 peptides, 51 chains. Longest chain 32 peptides. Score 0.532 Round 3: 419 peptides, 52 chains. Longest chain 32 peptides. Score 0.581 Round 4: 416 peptides, 51 chains. Longest chain 29 peptides. Score 0.583 Round 5: 406 peptides, 51 chains. Longest chain 33 peptides. Score 0.568 Taking the results from Round 4 Chains 52, Residues 365, Estimated correctness of the model 36.4 % 7 chains (77 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9632 restraints for refining 4835 atoms. 7932 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2738 (Rfree = 0.000) for 4835 atoms. Found 38 (43 requested) and removed 38 (21 requested) atoms. Cycle 22: After refmac, R = 0.2589 (Rfree = 0.000) for 4820 atoms. Found 14 (43 requested) and removed 28 (21 requested) atoms. Cycle 23: After refmac, R = 0.2559 (Rfree = 0.000) for 4791 atoms. Found 17 (43 requested) and removed 28 (21 requested) atoms. Cycle 24: After refmac, R = 0.2526 (Rfree = 0.000) for 4767 atoms. Found 20 (42 requested) and removed 27 (21 requested) atoms. Cycle 25: After refmac, R = 0.2470 (Rfree = 0.000) for 4753 atoms. Found 15 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4895 seeds are put forward NCS extension: 43 residues added (4 deleted due to clashes), 4938 seeds are put forward Round 1: 385 peptides, 60 chains. Longest chain 24 peptides. Score 0.467 Round 2: 409 peptides, 50 chains. Longest chain 25 peptides. Score 0.579 Round 3: 416 peptides, 51 chains. Longest chain 31 peptides. Score 0.583 Round 4: 411 peptides, 48 chains. Longest chain 31 peptides. Score 0.596 Round 5: 401 peptides, 53 chains. Longest chain 31 peptides. Score 0.546 Taking the results from Round 4 Chains 52, Residues 363, Estimated correctness of the model 40.0 % 5 chains (76 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9785 restraints for refining 4835 atoms. 8076 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2765 (Rfree = 0.000) for 4835 atoms. Found 43 (43 requested) and removed 38 (21 requested) atoms. Cycle 27: After refmac, R = 0.2526 (Rfree = 0.000) for 4831 atoms. Found 17 (43 requested) and removed 26 (21 requested) atoms. Cycle 28: After refmac, R = 0.2466 (Rfree = 0.000) for 4814 atoms. Found 12 (43 requested) and removed 25 (21 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 4794 atoms. Found 9 (43 requested) and removed 23 (21 requested) atoms. Cycle 30: After refmac, R = 0.2419 (Rfree = 0.000) for 4770 atoms. Found 15 (42 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4907 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 4929 seeds are put forward Round 1: 368 peptides, 58 chains. Longest chain 30 peptides. Score 0.453 Round 2: 407 peptides, 53 chains. Longest chain 34 peptides. Score 0.556 Round 3: 409 peptides, 54 chains. Longest chain 28 peptides. Score 0.552 Round 4: 431 peptides, 52 chains. Longest chain 36 peptides. Score 0.598 Round 5: 428 peptides, 52 chains. Longest chain 26 peptides. Score 0.594 Taking the results from Round 4 Chains 56, Residues 379, Estimated correctness of the model 40.5 % 5 chains (97 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9312 restraints for refining 4835 atoms. 7443 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 4835 atoms. Found 36 (43 requested) and removed 36 (21 requested) atoms. Cycle 32: After refmac, R = 0.2411 (Rfree = 0.000) for 4819 atoms. Found 15 (43 requested) and removed 27 (21 requested) atoms. Cycle 33: After refmac, R = 0.2352 (Rfree = 0.000) for 4804 atoms. Found 13 (43 requested) and removed 24 (21 requested) atoms. Cycle 34: After refmac, R = 0.2282 (Rfree = 0.000) for 4784 atoms. Found 11 (43 requested) and removed 23 (21 requested) atoms. Cycle 35: After refmac, R = 0.2277 (Rfree = 0.000) for 4761 atoms. Found 6 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 4914 seeds are put forward NCS extension: 53 residues added (6 deleted due to clashes), 4967 seeds are put forward Round 1: 375 peptides, 57 chains. Longest chain 27 peptides. Score 0.473 Round 2: 388 peptides, 49 chains. Longest chain 34 peptides. Score 0.554 Round 3: 397 peptides, 47 chains. Longest chain 35 peptides. Score 0.582 Round 4: 404 peptides, 48 chains. Longest chain 38 peptides. Score 0.586 Round 5: 406 peptides, 46 chains. Longest chain 51 peptides. Score 0.602 Taking the results from Round 5 Chains 48, Residues 360, Estimated correctness of the model 41.6 % 8 chains (114 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9301 restraints for refining 4835 atoms. 7483 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2645 (Rfree = 0.000) for 4835 atoms. Found 38 (43 requested) and removed 40 (21 requested) atoms. Cycle 37: After refmac, R = 0.2428 (Rfree = 0.000) for 4822 atoms. Found 11 (43 requested) and removed 27 (21 requested) atoms. Cycle 38: After refmac, R = 0.2359 (Rfree = 0.000) for 4797 atoms. Found 4 (43 requested) and removed 27 (21 requested) atoms. Cycle 39: After refmac, R = 0.2313 (Rfree = 0.000) for 4756 atoms. Found 7 (42 requested) and removed 23 (21 requested) atoms. Cycle 40: After refmac, R = 0.2326 (Rfree = 0.000) for 4735 atoms. Found 16 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 49 residues added (3 deleted due to clashes), 4906 seeds are put forward Round 1: 319 peptides, 49 chains. Longest chain 18 peptides. Score 0.435 Round 2: 381 peptides, 44 chains. Longest chain 35 peptides. Score 0.579 Round 3: 397 peptides, 51 chains. Longest chain 23 peptides. Score 0.554 Round 4: 401 peptides, 51 chains. Longest chain 28 peptides. Score 0.560 Round 5: 407 peptides, 48 chains. Longest chain 37 peptides. Score 0.590 Taking the results from Round 5 Chains 50, Residues 359, Estimated correctness of the model 38.3 % 6 chains (110 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9325 restraints for refining 4835 atoms. 7504 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2561 (Rfree = 0.000) for 4835 atoms. Found 36 (43 requested) and removed 45 (21 requested) atoms. Cycle 42: After refmac, R = 0.2444 (Rfree = 0.000) for 4815 atoms. Found 15 (43 requested) and removed 28 (21 requested) atoms. Cycle 43: After refmac, R = 0.2355 (Rfree = 0.000) for 4788 atoms. Found 18 (43 requested) and removed 23 (21 requested) atoms. Cycle 44: After refmac, R = 0.2310 (Rfree = 0.000) for 4768 atoms. Found 9 (42 requested) and removed 22 (21 requested) atoms. Cycle 45: After refmac, R = 0.2308 (Rfree = 0.000) for 4747 atoms. Found 8 (42 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 4879 seeds are put forward NCS extension: 48 residues added (7 deleted due to clashes), 4927 seeds are put forward Round 1: 337 peptides, 49 chains. Longest chain 22 peptides. Score 0.468 Round 2: 374 peptides, 44 chains. Longest chain 33 peptides. Score 0.568 Round 3: 370 peptides, 47 chains. Longest chain 33 peptides. Score 0.540 Round 4: 373 peptides, 43 chains. Longest chain 23 peptides. Score 0.574 Round 5: 356 peptides, 45 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 330, Estimated correctness of the model 33.9 % 5 chains (51 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (330 residues) following loop building 5 chains (51 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14494 reflections ( 99.68 % complete ) and 10128 restraints for refining 4834 atoms. 8692 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 4834 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2421 (Rfree = 0.000) for 4804 atoms. Found 0 (43 requested) and removed 8 (21 requested) atoms. Cycle 48: After refmac, R = 0.2367 (Rfree = 0.000) for 4790 atoms. Found 0 (43 requested) and removed 11 (21 requested) atoms. Cycle 49: After refmac, R = 0.2383 (Rfree = 0.000) for 4772 atoms. TimeTaking 65.53