null Sun 23 Dec 22:23:02 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 1vp4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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/1vp4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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 22:23:11 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/1vp4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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 663 and 0 Target number of residues in the AU: 663 Target solvent content: 0.6667 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-4.0-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 4.001 Wilson plot Bfac: 89.62 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 9154 reflections ( 99.65 % complete ) and 0 restraints for refining 7508 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3659 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3421 (Rfree = 0.000) for 7508 atoms. Found 35 (35 requested) and removed 102 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 7567 seeds are put forward NCS extension: 0 residues added, 7567 seeds are put forward Round 1: 268 peptides, 55 chains. Longest chain 8 peptides. Score 0.260 Round 2: 343 peptides, 61 chains. Longest chain 15 peptides. Score 0.345 Round 3: 400 peptides, 63 chains. Longest chain 13 peptides. Score 0.420 Round 4: 409 peptides, 66 chains. Longest chain 17 peptides. Score 0.414 Round 5: 412 peptides, 64 chains. Longest chain 20 peptides. Score 0.431 Taking the results from Round 5 Chains 64, Residues 348, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14622 restraints for refining 6140 atoms. 13294 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2817 (Rfree = 0.000) for 6140 atoms. Found 29 (29 requested) and removed 84 (14 requested) atoms. Cycle 2: After refmac, R = 0.2558 (Rfree = 0.000) for 5991 atoms. Found 22 (28 requested) and removed 52 (14 requested) atoms. Cycle 3: After refmac, R = 0.2507 (Rfree = 0.000) for 5889 atoms. Found 21 (28 requested) and removed 30 (14 requested) atoms. Cycle 4: After refmac, R = 0.2497 (Rfree = 0.000) for 5841 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 5: After refmac, R = 0.2369 (Rfree = 0.000) for 5791 atoms. Found 21 (27 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 5992 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6016 seeds are put forward Round 1: 337 peptides, 68 chains. Longest chain 10 peptides. Score 0.285 Round 2: 428 peptides, 72 chains. Longest chain 14 peptides. Score 0.403 Round 3: 416 peptides, 59 chains. Longest chain 17 peptides. Score 0.469 Round 4: 420 peptides, 60 chains. Longest chain 21 peptides. Score 0.468 Round 5: 426 peptides, 63 chains. Longest chain 19 peptides. Score 0.458 Taking the results from Round 3 Chains 60, Residues 357, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 13346 restraints for refining 5881 atoms. 11945 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2410 (Rfree = 0.000) for 5881 atoms. Found 25 (27 requested) and removed 59 (13 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 5806 atoms. Found 22 (27 requested) and removed 31 (13 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 5764 atoms. Found 9 (27 requested) and removed 23 (13 requested) atoms. Cycle 9: After refmac, R = 0.2214 (Rfree = 0.000) for 5723 atoms. Found 13 (27 requested) and removed 27 (13 requested) atoms. Cycle 10: After refmac, R = 0.1997 (Rfree = 0.000) for 5683 atoms. Found 4 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 5921 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5944 seeds are put forward Round 1: 361 peptides, 66 chains. Longest chain 12 peptides. Score 0.339 Round 2: 410 peptides, 63 chains. Longest chain 16 peptides. Score 0.435 Round 3: 416 peptides, 63 chains. Longest chain 17 peptides. Score 0.443 Round 4: 417 peptides, 53 chains. Longest chain 19 peptides. Score 0.507 Round 5: 423 peptides, 61 chains. Longest chain 24 peptides. Score 0.466 Taking the results from Round 4 Chains 55, Residues 364, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 13716 restraints for refining 6060 atoms. 12234 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2363 (Rfree = 0.000) for 6060 atoms. Found 28 (28 requested) and removed 51 (14 requested) atoms. Cycle 12: After refmac, R = 0.2121 (Rfree = 0.000) for 5997 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 13: After refmac, R = 0.1927 (Rfree = 0.000) for 5962 atoms. Found 14 (28 requested) and removed 20 (14 requested) atoms. Cycle 14: After refmac, R = 0.1948 (Rfree = 0.000) for 5941 atoms. Found 9 (28 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.1845 (Rfree = 0.000) for 5925 atoms. Found 2 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 6117 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6135 seeds are put forward Round 1: 387 peptides, 75 chains. Longest chain 9 peptides. Score 0.319 Round 2: 425 peptides, 65 chains. Longest chain 17 peptides. Score 0.444 Round 3: 421 peptides, 64 chains. Longest chain 16 peptides. Score 0.444 Round 4: 429 peptides, 65 chains. Longest chain 19 peptides. Score 0.449 Round 5: 412 peptides, 58 chains. Longest chain 19 peptides. Score 0.469 Taking the results from Round 5 Chains 58, Residues 354, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14514 restraints for refining 6139 atoms. 13156 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2417 (Rfree = 0.000) for 6139 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 17: After refmac, R = 0.2296 (Rfree = 0.000) for 6087 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 6024 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 19: After refmac, R = 0.2215 (Rfree = 0.000) for 5970 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 20: After refmac, R = 0.2264 (Rfree = 0.000) for 5934 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.40 Search for helices and strands: 0 residues in 0 chains, 6144 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6159 seeds are put forward Round 1: 314 peptides, 63 chains. Longest chain 15 peptides. Score 0.282 Round 2: 391 peptides, 66 chains. Longest chain 18 peptides. Score 0.386 Round 3: 403 peptides, 63 chains. Longest chain 17 peptides. Score 0.424 Round 4: 394 peptides, 60 chains. Longest chain 14 peptides. Score 0.431 Round 5: 399 peptides, 62 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 4 Chains 60, Residues 334, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14287 restraints for refining 6113 atoms. 13011 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2283 (Rfree = 0.000) for 6113 atoms. Found 29 (29 requested) and removed 59 (14 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 6026 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 23: After refmac, R = 0.2209 (Rfree = 0.000) for 5992 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 24: After refmac, R = 0.2201 (Rfree = 0.000) for 5949 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 25: After refmac, R = 0.1812 (Rfree = 0.000) for 5923 atoms. Found 11 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 6130 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6145 seeds are put forward Round 1: 286 peptides, 61 chains. Longest chain 8 peptides. Score 0.247 Round 2: 356 peptides, 67 chains. Longest chain 11 peptides. Score 0.324 Round 3: 374 peptides, 66 chains. Longest chain 12 peptides. Score 0.360 Round 4: 378 peptides, 64 chains. Longest chain 12 peptides. Score 0.380 Round 5: 381 peptides, 60 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Chains 60, Residues 321, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14333 restraints for refining 6118 atoms. 13109 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2136 (Rfree = 0.000) for 6118 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 27: After refmac, R = 0.2029 (Rfree = 0.000) for 6070 atoms. Found 16 (29 requested) and removed 20 (14 requested) atoms. Cycle 28: After refmac, R = 0.1902 (Rfree = 0.000) for 6045 atoms. Found 12 (28 requested) and removed 19 (14 requested) atoms. Cycle 29: After refmac, R = 0.2100 (Rfree = 0.000) for 6021 atoms. Found 22 (28 requested) and removed 27 (14 requested) atoms. Cycle 30: After refmac, R = 0.1894 (Rfree = 0.000) for 5994 atoms. Found 15 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 6220 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6237 seeds are put forward Round 1: 306 peptides, 64 chains. Longest chain 9 peptides. Score 0.260 Round 2: 377 peptides, 72 chains. Longest chain 14 peptides. Score 0.323 Round 3: 399 peptides, 69 chains. Longest chain 15 peptides. Score 0.379 Round 4: 383 peptides, 69 chains. Longest chain 11 peptides. Score 0.354 Round 5: 394 peptides, 66 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 66, Residues 328, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14308 restraints for refining 6140 atoms. 13062 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 6140 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 32: After refmac, R = 0.2068 (Rfree = 0.000) for 6115 atoms. Found 25 (29 requested) and removed 94 (14 requested) atoms. Cycle 33: After refmac, R = 0.1934 (Rfree = 0.000) for 6036 atoms. Found 10 (28 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1921 (Rfree = 0.000) for 6020 atoms. Found 9 (28 requested) and removed 30 (14 requested) atoms. Cycle 35: After refmac, R = 0.1890 (Rfree = 0.000) for 5992 atoms. Found 10 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 6207 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6220 seeds are put forward Round 1: 341 peptides, 70 chains. Longest chain 10 peptides. Score 0.277 Round 2: 392 peptides, 72 chains. Longest chain 13 peptides. Score 0.347 Round 3: 377 peptides, 69 chains. Longest chain 14 peptides. Score 0.344 Round 4: 371 peptides, 66 chains. Longest chain 13 peptides. Score 0.355 Round 5: 351 peptides, 62 chains. Longest chain 15 peptides. Score 0.351 Taking the results from Round 4 Chains 66, Residues 305, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14609 restraints for refining 6140 atoms. 13455 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2152 (Rfree = 0.000) for 6140 atoms. Found 24 (29 requested) and removed 56 (14 requested) atoms. Cycle 37: After refmac, R = 0.1999 (Rfree = 0.000) for 6067 atoms. Found 16 (29 requested) and removed 19 (14 requested) atoms. Cycle 38: After refmac, R = 0.1938 (Rfree = 0.000) for 6040 atoms. Found 14 (28 requested) and removed 20 (14 requested) atoms. Cycle 39: After refmac, R = 0.1769 (Rfree = 0.000) for 6019 atoms. Found 3 (28 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1857 (Rfree = 0.000) for 6000 atoms. Found 10 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 6175 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6188 seeds are put forward Round 1: 261 peptides, 55 chains. Longest chain 8 peptides. Score 0.247 Round 2: 305 peptides, 60 chains. Longest chain 10 peptides. Score 0.288 Round 3: 333 peptides, 60 chains. Longest chain 11 peptides. Score 0.336 Round 4: 344 peptides, 59 chains. Longest chain 17 peptides. Score 0.361 Round 5: 317 peptides, 53 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 4 Chains 59, Residues 285, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14574 restraints for refining 6139 atoms. 13471 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2017 (Rfree = 0.000) for 6139 atoms. Found 26 (29 requested) and removed 25 (14 requested) atoms. Cycle 42: After refmac, R = 0.2057 (Rfree = 0.000) for 6105 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 43: After refmac, R = 0.1977 (Rfree = 0.000) for 6070 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 44: After refmac, R = 0.2172 (Rfree = 0.000) for 6039 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 45: After refmac, R = 0.2001 (Rfree = 0.000) for 6004 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 6239 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6255 seeds are put forward Round 1: 222 peptides, 48 chains. Longest chain 9 peptides. Score 0.229 Round 2: 284 peptides, 58 chains. Longest chain 8 peptides. Score 0.266 Round 3: 292 peptides, 54 chains. Longest chain 14 peptides. Score 0.310 Round 4: 314 peptides, 55 chains. Longest chain 13 peptides. Score 0.340 Round 5: 301 peptides, 54 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 55, 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 1vp4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9154 reflections ( 99.65 % complete ) and 14226 restraints for refining 6031 atoms. 13245 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2018 (Rfree = 0.000) for 6031 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2051 (Rfree = 0.000) for 5975 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1922 (Rfree = 0.000) for 5936 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2061 (Rfree = 0.000) for 5906 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:47:53 GMT 2018 Job finished. TimeTaking 84.85 Used memory is bytes: 22803520