null Mon 24 Dec 07:29:32 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 2g0t-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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/2g0t-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 07:29:36 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/2g0t-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 853 and 0 Target number of residues in the AU: 853 Target solvent content: 0.6060 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 1.00 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: 29.560 3.800 Wilson plot Bfac: 55.01 12351 reflections ( 99.65 % complete ) and 0 restraints for refining 6184 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3102 (Rfree = 0.000) for 6184 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.61 Search for helices and strands: 0 residues in 0 chains, 6322 seeds are put forward NCS extension: 0 residues added, 6322 seeds are put forward Round 1: 391 peptides, 68 chains. Longest chain 14 peptides. Score 0.361 Round 2: 423 peptides, 54 chains. Longest chain 17 peptides. Score 0.490 Round 3: 442 peptides, 54 chains. Longest chain 21 peptides. Score 0.514 Round 4: 442 peptides, 51 chains. Longest chain 27 peptides. Score 0.530 Round 5: 446 peptides, 55 chains. Longest chain 23 peptides. Score 0.513 Taking the results from Round 4 Chains 56, Residues 391, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10776 restraints for refining 5066 atoms. 9158 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2983 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2738 (Rfree = 0.000) for 5013 atoms. Found 25 (27 requested) and removed 28 (13 requested) atoms. Cycle 3: After refmac, R = 0.2695 (Rfree = 0.000) for 4971 atoms. Found 23 (27 requested) and removed 23 (13 requested) atoms. Cycle 4: After refmac, R = 0.2630 (Rfree = 0.000) for 4944 atoms. Found 20 (27 requested) and removed 24 (13 requested) atoms. Cycle 5: After refmac, R = 0.2552 (Rfree = 0.000) for 4922 atoms. Found 18 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 2.58 Search for helices and strands: 0 residues in 0 chains, 5116 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 5141 seeds are put forward Round 1: 429 peptides, 55 chains. Longest chain 20 peptides. Score 0.492 Round 2: 464 peptides, 50 chains. Longest chain 26 peptides. Score 0.561 Round 3: 461 peptides, 51 chains. Longest chain 28 peptides. Score 0.553 Round 4: 461 peptides, 53 chains. Longest chain 25 peptides. Score 0.542 Round 5: 470 peptides, 54 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 2 Chains 52, Residues 414, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10478 restraints for refining 5066 atoms. 8665 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2715 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 7: After refmac, R = 0.2522 (Rfree = 0.000) for 5021 atoms. Found 24 (27 requested) and removed 32 (13 requested) atoms. Cycle 8: After refmac, R = 0.2521 (Rfree = 0.000) for 5001 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 9: After refmac, R = 0.2497 (Rfree = 0.000) for 4980 atoms. Found 25 (27 requested) and removed 31 (13 requested) atoms. Cycle 10: After refmac, R = 0.2504 (Rfree = 0.000) for 4967 atoms. Found 26 (27 requested) and removed 35 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 2.58 Search for helices and strands: 0 residues in 0 chains, 5143 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5156 seeds are put forward Round 1: 430 peptides, 55 chains. Longest chain 25 peptides. Score 0.493 Round 2: 451 peptides, 46 chains. Longest chain 38 peptides. Score 0.568 Round 3: 443 peptides, 51 chains. Longest chain 26 peptides. Score 0.532 Round 4: 455 peptides, 48 chains. Longest chain 30 peptides. Score 0.562 Round 5: 462 peptides, 47 chains. Longest chain 38 peptides. Score 0.575 Taking the results from Round 5 Chains 49, Residues 415, Estimated correctness of the model 0.0 % 6 chains (72 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10329 restraints for refining 5065 atoms. 8479 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2794 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 12: After refmac, R = 0.2654 (Rfree = 0.000) for 5014 atoms. Found 21 (27 requested) and removed 23 (13 requested) atoms. Cycle 13: After refmac, R = 0.2538 (Rfree = 0.000) for 4992 atoms. Found 18 (27 requested) and removed 37 (13 requested) atoms. Cycle 14: After refmac, R = 0.2497 (Rfree = 0.000) for 4962 atoms. Found 11 (27 requested) and removed 30 (13 requested) atoms. Cycle 15: After refmac, R = 0.2447 (Rfree = 0.000) for 4936 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 2.57 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5159 seeds are put forward Round 1: 421 peptides, 58 chains. Longest chain 28 peptides. Score 0.464 Round 2: 424 peptides, 50 chains. Longest chain 33 peptides. Score 0.514 Round 3: 453 peptides, 50 chains. Longest chain 30 peptides. Score 0.549 Round 4: 443 peptides, 51 chains. Longest chain 38 peptides. Score 0.532 Round 5: 453 peptides, 56 chains. Longest chain 27 peptides. Score 0.516 Taking the results from Round 3 Chains 51, Residues 403, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10459 restraints for refining 5065 atoms. 8751 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2676 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 17: After refmac, R = 0.2465 (Rfree = 0.000) for 5049 atoms. Found 12 (27 requested) and removed 33 (13 requested) atoms. Cycle 18: After refmac, R = 0.2417 (Rfree = 0.000) for 4998 atoms. Found 10 (27 requested) and removed 23 (13 requested) atoms. Cycle 19: After refmac, R = 0.2334 (Rfree = 0.000) for 4975 atoms. Found 6 (27 requested) and removed 30 (13 requested) atoms. Cycle 20: After refmac, R = 0.2318 (Rfree = 0.000) for 4933 atoms. Found 8 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5108 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5128 seeds are put forward Round 1: 411 peptides, 61 chains. Longest chain 23 peptides. Score 0.433 Round 2: 438 peptides, 50 chains. Longest chain 22 peptides. Score 0.531 Round 3: 446 peptides, 52 chains. Longest chain 29 peptides. Score 0.530 Round 4: 459 peptides, 54 chains. Longest chain 24 peptides. Score 0.534 Round 5: 453 peptides, 53 chains. Longest chain 28 peptides. Score 0.532 Taking the results from Round 4 Chains 58, Residues 405, Estimated correctness of the model 0.0 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10499 restraints for refining 5066 atoms. 8752 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2752 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 22: After refmac, R = 0.2562 (Rfree = 0.000) for 5043 atoms. Found 17 (27 requested) and removed 30 (13 requested) atoms. Cycle 23: After refmac, R = 0.2436 (Rfree = 0.000) for 5019 atoms. Found 8 (27 requested) and removed 23 (13 requested) atoms. Cycle 24: After refmac, R = 0.2349 (Rfree = 0.000) for 4990 atoms. Found 8 (27 requested) and removed 25 (13 requested) atoms. Cycle 25: After refmac, R = 0.2310 (Rfree = 0.000) for 4962 atoms. Found 4 (27 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5109 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 5126 seeds are put forward Round 1: 400 peptides, 57 chains. Longest chain 22 peptides. Score 0.442 Round 2: 459 peptides, 53 chains. Longest chain 24 peptides. Score 0.539 Round 3: 429 peptides, 51 chains. Longest chain 28 peptides. Score 0.515 Round 4: 451 peptides, 50 chains. Longest chain 27 peptides. Score 0.546 Round 5: 446 peptides, 53 chains. Longest chain 21 peptides. Score 0.524 Taking the results from Round 4 Chains 55, Residues 401, Estimated correctness of the model 0.0 % 5 chains (76 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10198 restraints for refining 5066 atoms. 8358 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2826 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 27: After refmac, R = 0.2635 (Rfree = 0.000) for 5033 atoms. Found 26 (27 requested) and removed 37 (13 requested) atoms. Cycle 28: After refmac, R = 0.2485 (Rfree = 0.000) for 4995 atoms. Found 15 (27 requested) and removed 30 (13 requested) atoms. Cycle 29: After refmac, R = 0.2469 (Rfree = 0.000) for 4963 atoms. Found 18 (27 requested) and removed 29 (13 requested) atoms. Cycle 30: After refmac, R = 0.2420 (Rfree = 0.000) for 4932 atoms. Found 9 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.57 Search for helices and strands: 0 residues in 0 chains, 5086 seeds are put forward NCS extension: 11 residues added (10 deleted due to clashes), 5097 seeds are put forward Round 1: 413 peptides, 61 chains. Longest chain 26 peptides. Score 0.435 Round 2: 468 peptides, 59 chains. Longest chain 23 peptides. Score 0.517 Round 3: 453 peptides, 56 chains. Longest chain 26 peptides. Score 0.516 Round 4: 448 peptides, 59 chains. Longest chain 28 peptides. Score 0.493 Round 5: 436 peptides, 52 chains. Longest chain 23 peptides. Score 0.517 Taking the results from Round 5 Chains 58, Residues 384, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10895 restraints for refining 5065 atoms. 9289 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2704 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 32: After refmac, R = 0.2544 (Rfree = 0.000) for 5022 atoms. Found 18 (27 requested) and removed 18 (13 requested) atoms. Cycle 33: After refmac, R = 0.2527 (Rfree = 0.000) for 5003 atoms. Found 11 (27 requested) and removed 26 (13 requested) atoms. Cycle 34: After refmac, R = 0.2471 (Rfree = 0.000) for 4976 atoms. Found 19 (27 requested) and removed 25 (13 requested) atoms. Cycle 35: After refmac, R = 0.2622 (Rfree = 0.000) for 4961 atoms. Found 17 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.58 Search for helices and strands: 0 residues in 0 chains, 5126 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 5140 seeds are put forward Round 1: 384 peptides, 63 chains. Longest chain 17 peptides. Score 0.382 Round 2: 417 peptides, 54 chains. Longest chain 26 peptides. Score 0.482 Round 3: 430 peptides, 58 chains. Longest chain 23 peptides. Score 0.475 Round 4: 422 peptides, 49 chains. Longest chain 17 peptides. Score 0.518 Round 5: 433 peptides, 58 chains. Longest chain 19 peptides. Score 0.479 Taking the results from Round 4 Chains 49, Residues 373, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 11233 restraints for refining 5065 atoms. 9751 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2960 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 37: After refmac, R = 0.2589 (Rfree = 0.000) for 5040 atoms. Found 23 (27 requested) and removed 21 (13 requested) atoms. Cycle 38: After refmac, R = 0.2538 (Rfree = 0.000) for 5020 atoms. Found 16 (27 requested) and removed 22 (13 requested) atoms. Cycle 39: After refmac, R = 0.2553 (Rfree = 0.000) for 5003 atoms. Found 14 (27 requested) and removed 26 (13 requested) atoms. Cycle 40: After refmac, R = 0.2499 (Rfree = 0.000) for 4986 atoms. Found 13 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 5146 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5158 seeds are put forward Round 1: 365 peptides, 57 chains. Longest chain 27 peptides. Score 0.393 Round 2: 424 peptides, 56 chains. Longest chain 26 peptides. Score 0.479 Round 3: 399 peptides, 56 chains. Longest chain 27 peptides. Score 0.447 Round 4: 426 peptides, 58 chains. Longest chain 17 peptides. Score 0.470 Round 5: 433 peptides, 58 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 5 Chains 60, Residues 375, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10906 restraints for refining 5066 atoms. 9324 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2806 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 42: After refmac, R = 0.2539 (Rfree = 0.000) for 5033 atoms. Found 21 (27 requested) and removed 26 (13 requested) atoms. Cycle 43: After refmac, R = 0.2482 (Rfree = 0.000) for 5011 atoms. Found 16 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2465 (Rfree = 0.000) for 4994 atoms. Found 26 (27 requested) and removed 25 (13 requested) atoms. Cycle 45: After refmac, R = 0.2422 (Rfree = 0.000) for 4986 atoms. Found 15 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5132 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5150 seeds are put forward Round 1: 362 peptides, 61 chains. Longest chain 19 peptides. Score 0.363 Round 2: 396 peptides, 54 chains. Longest chain 21 peptides. Score 0.455 Round 3: 425 peptides, 57 chains. Longest chain 23 peptides. Score 0.475 Round 4: 437 peptides, 55 chains. Longest chain 21 peptides. Score 0.502 Round 5: 408 peptides, 54 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 382, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (382 residues) following loop building 4 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12351 reflections ( 99.65 % complete ) and 11041 restraints for refining 5066 atoms. 9477 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2829 (Rfree = 0.000) for 5066 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2768 (Rfree = 0.000) for 5024 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2824 (Rfree = 0.000) for 4995 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2723 (Rfree = 0.000) for 4976 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:56:29 GMT 2018 Job finished. TimeTaking 146.96 Used memory is bytes: 13135520