Mon 24 Dec 07:37:50 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 2go7-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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/2go7-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 07:37:54 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/2go7-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 837 and 0 Target number of residues in the AU: 837 Target solvent content: 0.6307 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: 2go7-3.4-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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 3.400 Wilson plot Bfac: 66.73 16795 reflections ( 99.81 % complete ) and 0 restraints for refining 7358 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3557 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3229 (Rfree = 0.000) for 7358 atoms. Found 55 (55 requested) and removed 117 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.79 Search for helices and strands: 0 residues in 0 chains, 7448 seeds are put forward NCS extension: 0 residues added, 7448 seeds are put forward Round 1: 354 peptides, 63 chains. Longest chain 12 peptides. Score 0.333 Round 2: 480 peptides, 76 chains. Longest chain 17 peptides. Score 0.427 Round 3: 496 peptides, 70 chains. Longest chain 16 peptides. Score 0.480 Round 4: 500 peptides, 68 chains. Longest chain 17 peptides. Score 0.496 Round 5: 526 peptides, 68 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 5 Chains 68, Residues 458, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 13107 restraints for refining 6023 atoms. 11343 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 6023 atoms. Found 45 (45 requested) and removed 41 (22 requested) atoms. Cycle 2: After refmac, R = 0.2463 (Rfree = 0.000) for 5947 atoms. Found 24 (45 requested) and removed 33 (22 requested) atoms. Cycle 3: After refmac, R = 0.2341 (Rfree = 0.000) for 5910 atoms. Found 15 (44 requested) and removed 24 (22 requested) atoms. Cycle 4: After refmac, R = 0.2252 (Rfree = 0.000) for 5890 atoms. Found 12 (44 requested) and removed 23 (22 requested) atoms. Cycle 5: After refmac, R = 0.2222 (Rfree = 0.000) for 5860 atoms. Found 17 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6141 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 6152 seeds are put forward Round 1: 464 peptides, 73 chains. Longest chain 16 peptides. Score 0.424 Round 2: 528 peptides, 66 chains. Longest chain 21 peptides. Score 0.538 Round 3: 508 peptides, 66 chains. Longest chain 27 peptides. Score 0.516 Round 4: 523 peptides, 61 chains. Longest chain 23 peptides. Score 0.558 Round 5: 535 peptides, 64 chains. Longest chain 30 peptides. Score 0.556 Taking the results from Round 4 Chains 61, Residues 462, Estimated correctness of the model 14.4 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12818 restraints for refining 6021 atoms. 10933 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2579 (Rfree = 0.000) for 6021 atoms. Found 45 (45 requested) and removed 27 (22 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 6012 atoms. Found 20 (45 requested) and removed 24 (22 requested) atoms. Cycle 8: After refmac, R = 0.2319 (Rfree = 0.000) for 5995 atoms. Found 12 (45 requested) and removed 24 (22 requested) atoms. Cycle 9: After refmac, R = 0.2285 (Rfree = 0.000) for 5979 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. Cycle 10: After refmac, R = 0.2260 (Rfree = 0.000) for 5959 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.76 Search for helices and strands: 0 residues in 0 chains, 6198 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 6218 seeds are put forward Round 1: 484 peptides, 73 chains. Longest chain 17 peptides. Score 0.449 Round 2: 507 peptides, 65 chains. Longest chain 24 peptides. Score 0.520 Round 3: 494 peptides, 65 chains. Longest chain 19 peptides. Score 0.505 Round 4: 500 peptides, 54 chains. Longest chain 31 peptides. Score 0.568 Round 5: 513 peptides, 58 chains. Longest chain 20 peptides. Score 0.562 Taking the results from Round 4 Chains 54, Residues 446, Estimated correctness of the model 17.9 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12869 restraints for refining 6023 atoms. 11027 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2503 (Rfree = 0.000) for 6023 atoms. Found 34 (45 requested) and removed 30 (22 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 6002 atoms. Found 14 (45 requested) and removed 24 (22 requested) atoms. Cycle 13: After refmac, R = 0.2207 (Rfree = 0.000) for 5973 atoms. Found 9 (45 requested) and removed 25 (22 requested) atoms. Cycle 14: After refmac, R = 0.2154 (Rfree = 0.000) for 5948 atoms. Found 9 (44 requested) and removed 23 (22 requested) atoms. Cycle 15: After refmac, R = 0.2139 (Rfree = 0.000) for 5930 atoms. Found 6 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 6149 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 6166 seeds are put forward Round 1: 468 peptides, 70 chains. Longest chain 18 peptides. Score 0.446 Round 2: 494 peptides, 60 chains. Longest chain 21 peptides. Score 0.531 Round 3: 516 peptides, 58 chains. Longest chain 21 peptides. Score 0.565 Round 4: 510 peptides, 59 chains. Longest chain 22 peptides. Score 0.554 Round 5: 527 peptides, 63 chains. Longest chain 18 peptides. Score 0.552 Taking the results from Round 3 Chains 58, Residues 458, Estimated correctness of the model 16.8 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 13075 restraints for refining 6023 atoms. 11253 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 6023 atoms. Found 33 (45 requested) and removed 27 (22 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 6000 atoms. Found 11 (45 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2075 (Rfree = 0.000) for 5973 atoms. Found 3 (45 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2054 (Rfree = 0.000) for 5944 atoms. Found 8 (44 requested) and removed 24 (22 requested) atoms. Cycle 20: After refmac, R = 0.2034 (Rfree = 0.000) for 5925 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.73 Search for helices and strands: 0 residues in 0 chains, 6189 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6209 seeds are put forward Round 1: 475 peptides, 69 chains. Longest chain 23 peptides. Score 0.460 Round 2: 506 peptides, 59 chains. Longest chain 19 peptides. Score 0.549 Round 3: 509 peptides, 63 chains. Longest chain 22 peptides. Score 0.532 Round 4: 514 peptides, 58 chains. Longest chain 23 peptides. Score 0.563 Round 5: 514 peptides, 62 chains. Longest chain 21 peptides. Score 0.543 Taking the results from Round 4 Chains 59, Residues 456, Estimated correctness of the model 16.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12882 restraints for refining 6023 atoms. 11078 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 6023 atoms. Found 26 (45 requested) and removed 25 (22 requested) atoms. Cycle 22: After refmac, R = 0.2239 (Rfree = 0.000) for 6005 atoms. Found 22 (45 requested) and removed 24 (22 requested) atoms. Cycle 23: After refmac, R = 0.2186 (Rfree = 0.000) for 5998 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2151 (Rfree = 0.000) for 5978 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. Cycle 25: After refmac, R = 0.2129 (Rfree = 0.000) for 5963 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 6221 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6242 seeds are put forward Round 1: 471 peptides, 67 chains. Longest chain 24 peptides. Score 0.466 Round 2: 519 peptides, 62 chains. Longest chain 24 peptides. Score 0.548 Round 3: 516 peptides, 66 chains. Longest chain 28 peptides. Score 0.525 Round 4: 529 peptides, 63 chains. Longest chain 26 peptides. Score 0.554 Round 5: 504 peptides, 63 chains. Longest chain 20 peptides. Score 0.527 Taking the results from Round 4 Chains 66, Residues 466, Estimated correctness of the model 13.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12615 restraints for refining 6023 atoms. 10659 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2427 (Rfree = 0.000) for 6023 atoms. Found 43 (45 requested) and removed 27 (22 requested) atoms. Cycle 27: After refmac, R = 0.2234 (Rfree = 0.000) for 6011 atoms. Found 17 (45 requested) and removed 24 (22 requested) atoms. Cycle 28: After refmac, R = 0.2164 (Rfree = 0.000) for 5991 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2118 (Rfree = 0.000) for 5975 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 5960 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6178 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6198 seeds are put forward Round 1: 443 peptides, 67 chains. Longest chain 24 peptides. Score 0.431 Round 2: 495 peptides, 69 chains. Longest chain 19 peptides. Score 0.484 Round 3: 493 peptides, 68 chains. Longest chain 22 peptides. Score 0.487 Round 4: 512 peptides, 68 chains. Longest chain 17 peptides. Score 0.510 Round 5: 509 peptides, 63 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 5 Chains 65, Residues 446, Estimated correctness of the model 4.9 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12798 restraints for refining 6022 atoms. 10981 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2466 (Rfree = 0.000) for 6022 atoms. Found 35 (45 requested) and removed 24 (22 requested) atoms. Cycle 32: After refmac, R = 0.2274 (Rfree = 0.000) for 6013 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. Cycle 33: After refmac, R = 0.2198 (Rfree = 0.000) for 5990 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2169 (Rfree = 0.000) for 5971 atoms. Found 7 (45 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.2144 (Rfree = 0.000) for 5954 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 2.76 Search for helices and strands: 0 residues in 0 chains, 6197 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 6212 seeds are put forward Round 1: 444 peptides, 71 chains. Longest chain 17 peptides. Score 0.409 Round 2: 521 peptides, 68 chains. Longest chain 20 peptides. Score 0.520 Round 3: 510 peptides, 68 chains. Longest chain 20 peptides. Score 0.507 Round 4: 497 peptides, 64 chains. Longest chain 24 peptides. Score 0.514 Round 5: 513 peptides, 61 chains. Longest chain 27 peptides. Score 0.547 Taking the results from Round 5 Chains 63, Residues 452, Estimated correctness of the model 10.4 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12573 restraints for refining 6022 atoms. 10645 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2454 (Rfree = 0.000) for 6022 atoms. Found 29 (45 requested) and removed 31 (22 requested) atoms. Cycle 37: After refmac, R = 0.2288 (Rfree = 0.000) for 5998 atoms. Found 11 (45 requested) and removed 24 (22 requested) atoms. Cycle 38: After refmac, R = 0.2247 (Rfree = 0.000) for 5975 atoms. Found 5 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.2239 (Rfree = 0.000) for 5952 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2236 (Rfree = 0.000) for 5932 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.77 Search for helices and strands: 0 residues in 0 chains, 6154 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6173 seeds are put forward Round 1: 453 peptides, 77 chains. Longest chain 16 peptides. Score 0.386 Round 2: 484 peptides, 68 chains. Longest chain 20 peptides. Score 0.477 Round 3: 502 peptides, 70 chains. Longest chain 18 peptides. Score 0.487 Round 4: 503 peptides, 64 chains. Longest chain 23 peptides. Score 0.520 Round 5: 499 peptides, 70 chains. Longest chain 25 peptides. Score 0.484 Taking the results from Round 4 Chains 65, Residues 439, Estimated correctness of the model 0.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12984 restraints for refining 6023 atoms. 11194 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2508 (Rfree = 0.000) for 6023 atoms. Found 33 (45 requested) and removed 24 (22 requested) atoms. Cycle 42: After refmac, R = 0.2273 (Rfree = 0.000) for 6018 atoms. Found 13 (45 requested) and removed 23 (22 requested) atoms. Cycle 43: After refmac, R = 0.2213 (Rfree = 0.000) for 5999 atoms. Found 11 (45 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.2154 (Rfree = 0.000) for 5982 atoms. Found 6 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.2133 (Rfree = 0.000) for 5963 atoms. Found 8 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6197 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6223 seeds are put forward Round 1: 422 peptides, 72 chains. Longest chain 15 peptides. Score 0.373 Round 2: 476 peptides, 68 chains. Longest chain 17 peptides. Score 0.467 Round 3: 467 peptides, 65 chains. Longest chain 32 peptides. Score 0.472 Round 4: 444 peptides, 59 chains. Longest chain 18 peptides. Score 0.478 Round 5: 455 peptides, 57 chains. Longest chain 19 peptides. Score 0.502 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 398, 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 2go7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16795 reflections ( 99.81 % complete ) and 13592 restraints for refining 6023 atoms. 12057 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2314 (Rfree = 0.000) for 6023 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2102 (Rfree = 0.000) for 5984 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2030 (Rfree = 0.000) for 5949 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 5926 atoms. TimeTaking 66.12