Sun 23 Dec 22:22:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2go7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2go7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2go7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-parrot-hancs ############### 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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-parrot-hancs/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 753 and 0 Target number of residues in the AU: 753 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-4.0-parrot-hancs.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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.15 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: 134.234 4.001 Wilson plot Bfac: 90.68 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 10348 reflections ( 99.71 % complete ) and 0 restraints for refining 7305 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3609 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3576 (Rfree = 0.000) for 7305 atoms. Found 34 (34 requested) and removed 39 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.11 Search for helices and strands: 0 residues in 0 chains, 7440 seeds are put forward NCS extension: 0 residues added, 7440 seeds are put forward Round 1: 294 peptides, 57 chains. Longest chain 9 peptides. Score 0.281 Round 2: 387 peptides, 61 chains. Longest chain 19 peptides. Score 0.392 Round 3: 414 peptides, 61 chains. Longest chain 21 peptides. Score 0.428 Round 4: 448 peptides, 62 chains. Longest chain 21 peptides. Score 0.466 Round 5: 446 peptides, 62 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 4 Chains 64, Residues 386, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13743 restraints for refining 5978 atoms. 12230 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2828 (Rfree = 0.000) for 5978 atoms. Found 28 (28 requested) and removed 44 (14 requested) atoms. Cycle 2: After refmac, R = 0.2640 (Rfree = 0.000) for 5809 atoms. Found 25 (28 requested) and removed 40 (14 requested) atoms. Cycle 3: After refmac, R = 0.2612 (Rfree = 0.000) for 5715 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 4: After refmac, R = 0.2446 (Rfree = 0.000) for 5645 atoms. Found 27 (27 requested) and removed 35 (13 requested) atoms. Cycle 5: After refmac, R = 0.2399 (Rfree = 0.000) for 5586 atoms. Found 23 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 5873 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5894 seeds are put forward Round 1: 394 peptides, 69 chains. Longest chain 15 peptides. Score 0.353 Round 2: 439 peptides, 64 chains. Longest chain 20 peptides. Score 0.443 Round 3: 450 peptides, 61 chains. Longest chain 15 peptides. Score 0.474 Round 4: 446 peptides, 66 chains. Longest chain 15 peptides. Score 0.440 Round 5: 462 peptides, 60 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 5 Chains 60, Residues 402, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13251 restraints for refining 5942 atoms. 11669 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2576 (Rfree = 0.000) for 5942 atoms. Found 28 (28 requested) and removed 58 (14 requested) atoms. Cycle 7: After refmac, R = 0.2440 (Rfree = 0.000) for 5812 atoms. Found 28 (28 requested) and removed 51 (14 requested) atoms. Cycle 8: After refmac, R = 0.2364 (Rfree = 0.000) for 5734 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 9: After refmac, R = 0.2252 (Rfree = 0.000) for 5683 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 10: After refmac, R = 0.2147 (Rfree = 0.000) for 5645 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 5909 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5930 seeds are put forward Round 1: 414 peptides, 70 chains. Longest chain 12 peptides. Score 0.374 Round 2: 452 peptides, 63 chains. Longest chain 17 peptides. Score 0.465 Round 3: 449 peptides, 63 chains. Longest chain 17 peptides. Score 0.461 Round 4: 446 peptides, 55 chains. Longest chain 22 peptides. Score 0.502 Round 5: 461 peptides, 60 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 4 Chains 55, Residues 391, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13376 restraints for refining 5981 atoms. 11867 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2388 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 47 (14 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 5904 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 13: After refmac, R = 0.2126 (Rfree = 0.000) for 5839 atoms. Found 25 (28 requested) and removed 20 (14 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 5807 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2086 (Rfree = 0.000) for 5779 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.19 Search for helices and strands: 0 residues in 0 chains, 6124 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6146 seeds are put forward Round 1: 391 peptides, 65 chains. Longest chain 15 peptides. Score 0.373 Round 2: 448 peptides, 62 chains. Longest chain 18 peptides. Score 0.466 Round 3: 466 peptides, 63 chains. Longest chain 22 peptides. Score 0.482 Round 4: 458 peptides, 60 chains. Longest chain 19 peptides. Score 0.489 Round 5: 460 peptides, 59 chains. Longest chain 20 peptides. Score 0.497 Taking the results from Round 5 Chains 62, Residues 401, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13218 restraints for refining 5982 atoms. 11593 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2569 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 17: After refmac, R = 0.2328 (Rfree = 0.000) for 5899 atoms. Found 26 (28 requested) and removed 28 (14 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 5856 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2216 (Rfree = 0.000) for 5827 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2230 (Rfree = 0.000) for 5810 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 6043 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6061 seeds are put forward Round 1: 380 peptides, 70 chains. Longest chain 15 peptides. Score 0.326 Round 2: 424 peptides, 63 chains. Longest chain 18 peptides. Score 0.429 Round 3: 438 peptides, 65 chains. Longest chain 17 peptides. Score 0.436 Round 4: 431 peptides, 64 chains. Longest chain 16 peptides. Score 0.433 Round 5: 427 peptides, 64 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 3 Chains 66, Residues 373, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13121 restraints for refining 5981 atoms. 11628 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2425 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Cycle 22: After refmac, R = 0.2198 (Rfree = 0.000) for 5918 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 23: After refmac, R = 0.1855 (Rfree = 0.000) for 5879 atoms. Found 8 (28 requested) and removed 20 (14 requested) atoms. Cycle 24: After refmac, R = 0.1973 (Rfree = 0.000) for 5834 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 25: After refmac, R = 0.1754 (Rfree = 0.000) for 5816 atoms. Found 4 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 6033 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 6060 seeds are put forward Round 1: 383 peptides, 70 chains. Longest chain 12 peptides. Score 0.331 Round 2: 435 peptides, 64 chains. Longest chain 18 peptides. Score 0.438 Round 3: 447 peptides, 65 chains. Longest chain 18 peptides. Score 0.447 Round 4: 458 peptides, 63 chains. Longest chain 19 peptides. Score 0.472 Round 5: 455 peptides, 68 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 4 Chains 63, Residues 395, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13522 restraints for refining 5981 atoms. 12005 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2557 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Cycle 27: After refmac, R = 0.2125 (Rfree = 0.000) for 5907 atoms. Found 27 (28 requested) and removed 23 (14 requested) atoms. Cycle 28: After refmac, R = 0.2067 (Rfree = 0.000) for 5876 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 29: After refmac, R = 0.1951 (Rfree = 0.000) for 5859 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 5859 atoms. Found 23 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 6131 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6146 seeds are put forward Round 1: 348 peptides, 66 chains. Longest chain 14 peptides. Score 0.304 Round 2: 387 peptides, 65 chains. Longest chain 14 peptides. Score 0.367 Round 3: 398 peptides, 58 chains. Longest chain 15 peptides. Score 0.425 Round 4: 425 peptides, 60 chains. Longest chain 19 peptides. Score 0.448 Round 5: 407 peptides, 63 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 4 Chains 60, Residues 365, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13727 restraints for refining 5982 atoms. 12327 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2545 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 32: After refmac, R = 0.2305 (Rfree = 0.000) for 5912 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 33: After refmac, R = 0.2224 (Rfree = 0.000) for 5871 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.2320 (Rfree = 0.000) for 5842 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.2077 (Rfree = 0.000) for 5816 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 6067 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6086 seeds are put forward Round 1: 341 peptides, 66 chains. Longest chain 12 peptides. Score 0.294 Round 2: 393 peptides, 63 chains. Longest chain 15 peptides. Score 0.388 Round 3: 381 peptides, 62 chains. Longest chain 14 peptides. Score 0.378 Round 4: 380 peptides, 61 chains. Longest chain 18 peptides. Score 0.382 Round 5: 410 peptides, 63 chains. Longest chain 22 peptides. Score 0.411 Taking the results from Round 5 Chains 63, Residues 347, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13537 restraints for refining 5980 atoms. 12101 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2493 (Rfree = 0.000) for 5980 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 37: After refmac, R = 0.2362 (Rfree = 0.000) for 5907 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 5868 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 5836 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 40: After refmac, R = 0.2056 (Rfree = 0.000) for 5820 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 6023 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 6054 seeds are put forward Round 1: 362 peptides, 70 chains. Longest chain 11 peptides. Score 0.300 Round 2: 390 peptides, 64 chains. Longest chain 13 peptides. Score 0.378 Round 3: 404 peptides, 65 chains. Longest chain 12 peptides. Score 0.391 Round 4: 405 peptides, 62 chains. Longest chain 13 peptides. Score 0.410 Round 5: 386 peptides, 58 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 4 Chains 62, Residues 343, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13610 restraints for refining 5978 atoms. 12300 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2420 (Rfree = 0.000) for 5978 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Cycle 42: After refmac, R = 0.2343 (Rfree = 0.000) for 5907 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.2242 (Rfree = 0.000) for 5870 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 44: After refmac, R = 0.2042 (Rfree = 0.000) for 5839 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 5835 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 6062 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6076 seeds are put forward Round 1: 325 peptides, 69 chains. Longest chain 12 peptides. Score 0.249 Round 2: 355 peptides, 62 chains. Longest chain 12 peptides. Score 0.341 Round 3: 366 peptides, 59 chains. Longest chain 17 peptides. Score 0.375 Round 4: 372 peptides, 54 chains. Longest chain 16 peptides. Score 0.414 Round 5: 385 peptides, 56 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 329, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2go7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10348 reflections ( 99.71 % complete ) and 13846 restraints for refining 5982 atoms. 12557 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2481 (Rfree = 0.000) for 5982 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2244 (Rfree = 0.000) for 5919 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2148 (Rfree = 0.000) for 5885 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1844 (Rfree = 0.000) for 5861 atoms. TimeTaking 83.02