Mon 24 Dec 07:43:25 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 2go7-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2go7-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2go7-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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/2go7-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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 07:43:29 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/2go7-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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 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-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-4.0-parrot-noncs.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 7374 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3660 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3621 (Rfree = 0.000) for 7374 atoms. Found 35 (35 requested) and removed 46 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.07 Search for helices and strands: 0 residues in 0 chains, 7500 seeds are put forward NCS extension: 0 residues added, 7500 seeds are put forward Round 1: 268 peptides, 54 chains. Longest chain 10 peptides. Score 0.260 Round 2: 382 peptides, 62 chains. Longest chain 15 peptides. Score 0.379 Round 3: 451 peptides, 64 chains. Longest chain 18 peptides. Score 0.458 Round 4: 465 peptides, 65 chains. Longest chain 22 peptides. Score 0.470 Round 5: 480 peptides, 61 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 61, Residues 419, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13164 restraints for refining 5979 atoms. 11423 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2983 (Rfree = 0.000) for 5979 atoms. Found 28 (28 requested) and removed 73 (14 requested) atoms. Cycle 2: After refmac, R = 0.2831 (Rfree = 0.000) for 5788 atoms. Found 28 (28 requested) and removed 43 (14 requested) atoms. Cycle 3: After refmac, R = 0.2478 (Rfree = 0.000) for 5659 atoms. Found 22 (27 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2812 (Rfree = 0.000) for 5594 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Cycle 5: After refmac, R = 0.2667 (Rfree = 0.000) for 5518 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 5747 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5765 seeds are put forward Round 1: 417 peptides, 71 chains. Longest chain 16 peptides. Score 0.372 Round 2: 444 peptides, 60 chains. Longest chain 16 peptides. Score 0.472 Round 3: 449 peptides, 57 chains. Longest chain 24 peptides. Score 0.495 Round 4: 453 peptides, 62 chains. Longest chain 18 peptides. Score 0.472 Round 5: 466 peptides, 58 chains. Longest chain 23 peptides. Score 0.509 Taking the results from Round 5 Chains 58, Residues 408, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 12853 restraints for refining 5880 atoms. 11237 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2749 (Rfree = 0.000) for 5880 atoms. Found 27 (27 requested) and removed 100 (13 requested) atoms. Cycle 7: After refmac, R = 0.2582 (Rfree = 0.000) for 5701 atoms. Found 27 (27 requested) and removed 47 (13 requested) atoms. Cycle 8: After refmac, R = 0.2600 (Rfree = 0.000) for 5604 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 9: After refmac, R = 0.2515 (Rfree = 0.000) for 5519 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 10: After refmac, R = 0.2463 (Rfree = 0.000) for 5465 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.21 Search for helices and strands: 0 residues in 0 chains, 5661 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 5681 seeds are put forward Round 1: 392 peptides, 66 chains. Longest chain 22 peptides. Score 0.368 Round 2: 459 peptides, 65 chains. Longest chain 26 peptides. Score 0.462 Round 3: 446 peptides, 60 chains. Longest chain 25 peptides. Score 0.474 Round 4: 453 peptides, 58 chains. Longest chain 23 peptides. Score 0.494 Round 5: 467 peptides, 60 chains. Longest chain 24 peptides. Score 0.500 Taking the results from Round 5 Chains 60, Residues 407, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13396 restraints for refining 5980 atoms. 11828 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 5980 atoms. Found 28 (28 requested) and removed 48 (14 requested) atoms. Cycle 12: After refmac, R = 0.2520 (Rfree = 0.000) for 5885 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2292 (Rfree = 0.000) for 5816 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 5769 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 15: After refmac, R = 0.2267 (Rfree = 0.000) for 5744 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.85 3.22 Search for helices and strands: 0 residues in 0 chains, 6023 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6046 seeds are put forward Round 1: 388 peptides, 68 chains. Longest chain 13 peptides. Score 0.350 Round 2: 432 peptides, 63 chains. Longest chain 19 peptides. Score 0.440 Round 3: 440 peptides, 61 chains. Longest chain 15 peptides. Score 0.461 Round 4: 446 peptides, 59 chains. Longest chain 22 peptides. Score 0.480 Round 5: 443 peptides, 59 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 4 Chains 59, Residues 387, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13305 restraints for refining 5982 atoms. 11740 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2529 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 53 (14 requested) atoms. Cycle 17: After refmac, R = 0.2426 (Rfree = 0.000) for 5882 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 18: After refmac, R = 0.2325 (Rfree = 0.000) for 5806 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 19: After refmac, R = 0.2310 (Rfree = 0.000) for 5754 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 5721 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.21 Search for helices and strands: 0 residues in 0 chains, 5960 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5980 seeds are put forward Round 1: 359 peptides, 68 chains. Longest chain 11 peptides. Score 0.308 Round 2: 404 peptides, 66 chains. Longest chain 14 peptides. Score 0.385 Round 3: 406 peptides, 61 chains. Longest chain 14 peptides. Score 0.418 Round 4: 439 peptides, 62 chains. Longest chain 16 peptides. Score 0.454 Round 5: 434 peptides, 63 chains. Longest chain 17 peptides. Score 0.442 Taking the results from Round 4 Chains 62, Residues 377, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13158 restraints for refining 5900 atoms. 11712 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2535 (Rfree = 0.000) for 5900 atoms. Found 28 (28 requested) and removed 113 (14 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2309 (Rfree = 0.000) for 5755 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2197 (Rfree = 0.000) for 5723 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2184 (Rfree = 0.000) for 5689 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 25: After refmac, R = 0.2224 (Rfree = 0.000) for 5664 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 5953 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5970 seeds are put forward Round 1: 347 peptides, 68 chains. Longest chain 11 peptides. Score 0.290 Round 2: 425 peptides, 68 chains. Longest chain 13 peptides. Score 0.401 Round 3: 419 peptides, 65 chains. Longest chain 17 peptides. Score 0.411 Round 4: 432 peptides, 64 chains. Longest chain 23 peptides. Score 0.434 Round 5: 427 peptides, 62 chains. Longest chain 20 peptides. Score 0.439 Taking the results from Round 5 Chains 62, Residues 365, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13715 restraints for refining 5982 atoms. 12317 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2507 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 27: After refmac, R = 0.2355 (Rfree = 0.000) for 5889 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 28: After refmac, R = 0.2153 (Rfree = 0.000) for 5860 atoms. Found 22 (27 requested) and removed 25 (13 requested) atoms. Cycle 29: After refmac, R = 0.2079 (Rfree = 0.000) for 5824 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 30: After refmac, R = 0.1967 (Rfree = 0.000) for 5785 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 6017 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6035 seeds are put forward Round 1: 350 peptides, 68 chains. Longest chain 12 peptides. Score 0.294 Round 2: 404 peptides, 67 chains. Longest chain 15 peptides. Score 0.379 Round 3: 407 peptides, 65 chains. Longest chain 15 peptides. Score 0.395 Round 4: 426 peptides, 61 chains. Longest chain 19 peptides. Score 0.444 Round 5: 431 peptides, 62 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 5 Chains 62, Residues 369, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13453 restraints for refining 5981 atoms. 12039 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2156 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 32: After refmac, R = 0.2053 (Rfree = 0.000) for 5930 atoms. Found 28 (28 requested) and removed 47 (14 requested) atoms. Cycle 33: After refmac, R = 0.2015 (Rfree = 0.000) for 5888 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 34: After refmac, R = 0.1950 (Rfree = 0.000) for 5850 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 35: After refmac, R = 0.1993 (Rfree = 0.000) for 5822 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.14 Search for helices and strands: 0 residues in 0 chains, 6037 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6054 seeds are put forward Round 1: 322 peptides, 62 chains. Longest chain 15 peptides. Score 0.291 Round 2: 384 peptides, 67 chains. Longest chain 15 peptides. Score 0.351 Round 3: 387 peptides, 63 chains. Longest chain 17 peptides. Score 0.380 Round 4: 412 peptides, 66 chains. Longest chain 14 peptides. Score 0.396 Round 5: 405 peptides, 65 chains. Longest chain 16 peptides. Score 0.392 Taking the results from Round 4 Chains 67, Residues 346, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13598 restraints for refining 5981 atoms. 12248 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2037 (Rfree = 0.000) for 5981 atoms. Found 25 (28 requested) and removed 24 (14 requested) atoms. Cycle 37: After refmac, R = 0.1944 (Rfree = 0.000) for 5927 atoms. Found 20 (28 requested) and removed 28 (14 requested) atoms. Cycle 38: After refmac, R = 0.1684 (Rfree = 0.000) for 5893 atoms. Found 12 (28 requested) and removed 21 (14 requested) atoms. Cycle 39: After refmac, R = 0.1763 (Rfree = 0.000) for 5863 atoms. Found 19 (27 requested) and removed 20 (13 requested) atoms. Cycle 40: After refmac, R = 0.1929 (Rfree = 0.000) for 5853 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.13 Search for helices and strands: 0 residues in 0 chains, 6076 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6096 seeds are put forward Round 1: 358 peptides, 70 chains. Longest chain 14 peptides. Score 0.294 Round 2: 377 peptides, 64 chains. Longest chain 13 peptides. Score 0.359 Round 3: 391 peptides, 66 chains. Longest chain 16 peptides. Score 0.367 Round 4: 389 peptides, 64 chains. Longest chain 15 peptides. Score 0.376 Round 5: 396 peptides, 62 chains. Longest chain 18 peptides. Score 0.398 Taking the results from Round 5 Chains 62, Residues 334, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13805 restraints for refining 5982 atoms. 12531 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2363 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 45 (14 requested) atoms. Cycle 42: After refmac, R = 0.2127 (Rfree = 0.000) for 5926 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 5902 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 44: After refmac, R = 0.1975 (Rfree = 0.000) for 5881 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 45: After refmac, R = 0.1613 (Rfree = 0.000) for 5857 atoms. Found 7 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 6071 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 6104 seeds are put forward Round 1: 284 peptides, 58 chains. Longest chain 11 peptides. Score 0.258 Round 2: 316 peptides, 54 chains. Longest chain 14 peptides. Score 0.335 Round 3: 309 peptides, 50 chains. Longest chain 18 peptides. Score 0.351 Round 4: 292 peptides, 48 chains. Longest chain 18 peptides. Score 0.339 Round 5: 299 peptides, 48 chains. Longest chain 25 peptides. Score 0.350 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % 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 14159 restraints for refining 5981 atoms. 13173 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2073 (Rfree = 0.000) for 5981 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2119 (Rfree = 0.000) for 5937 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1966 (Rfree = 0.000) for 5887 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2025 (Rfree = 0.000) for 5853 atoms. TimeTaking 65.43