Mon 24 Dec 07:49:55 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 1vp4-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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/1vp4-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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 07:50:00 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/1vp4-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-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 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-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.85 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 7500 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3373 (Rfree = 0.000) for 7500 atoms. Found 25 (35 requested) and removed 48 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 7593 seeds are put forward NCS extension: 0 residues added, 7593 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 11 peptides. Score 0.250 Round 2: 314 peptides, 54 chains. Longest chain 16 peptides. Score 0.348 Round 3: 359 peptides, 59 chains. Longest chain 16 peptides. Score 0.384 Round 4: 369 peptides, 61 chains. Longest chain 16 peptides. Score 0.386 Round 5: 391 peptides, 59 chains. Longest chain 18 peptides. Score 0.433 Taking the results from Round 5 Chains 59, Residues 332, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14344 restraints for refining 6034 atoms. 13051 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2882 (Rfree = 0.000) for 6034 atoms. Found 26 (28 requested) and removed 43 (14 requested) atoms. Cycle 2: After refmac, R = 0.2818 (Rfree = 0.000) for 5919 atoms. Found 28 (28 requested) and removed 43 (14 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2942 (Rfree = 0.000) for 5839 atoms. Found 24 (28 requested) and removed 39 (14 requested) atoms. Cycle 4: After refmac, R = 0.2456 (Rfree = 0.000) for 5747 atoms. Found 13 (27 requested) and removed 31 (13 requested) atoms. Cycle 5: After refmac, R = 0.2622 (Rfree = 0.000) for 5671 atoms. Found 20 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.48 Search for helices and strands: 0 residues in 0 chains, 5850 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 5888 seeds are put forward Round 1: 326 peptides, 62 chains. Longest chain 10 peptides. Score 0.310 Round 2: 382 peptides, 62 chains. Longest chain 16 peptides. Score 0.399 Round 3: 399 peptides, 62 chains. Longest chain 19 peptides. Score 0.425 Round 4: 412 peptides, 60 chains. Longest chain 16 peptides. Score 0.457 Round 5: 401 peptides, 59 chains. Longest chain 17 peptides. Score 0.447 Taking the results from Round 4 Chains 60, Residues 352, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 12610 restraints for refining 5610 atoms. 11209 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2614 (Rfree = 0.000) for 5610 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. Cycle 7: After refmac, R = 0.2351 (Rfree = 0.000) for 5528 atoms. Found 26 (26 requested) and removed 33 (13 requested) atoms. Cycle 8: After refmac, R = 0.2112 (Rfree = 0.000) for 5490 atoms. Found 13 (26 requested) and removed 26 (13 requested) atoms. Cycle 9: After refmac, R = 0.2056 (Rfree = 0.000) for 5459 atoms. Found 5 (26 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 5434 atoms. Found 12 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.43 Search for helices and strands: 0 residues in 0 chains, 5634 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5659 seeds are put forward Round 1: 371 peptides, 68 chains. Longest chain 12 peptides. Score 0.341 Round 2: 397 peptides, 59 chains. Longest chain 19 peptides. Score 0.442 Round 3: 406 peptides, 63 chains. Longest chain 13 peptides. Score 0.429 Round 4: 410 peptides, 61 chains. Longest chain 16 peptides. Score 0.447 Round 5: 397 peptides, 59 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 4 Chains 62, Residues 349, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 13201 restraints for refining 5859 atoms. 11776 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2276 (Rfree = 0.000) for 5859 atoms. Found 24 (27 requested) and removed 110 (13 requested) atoms. Cycle 12: After refmac, R = 0.2297 (Rfree = 0.000) for 5730 atoms. Found 18 (27 requested) and removed 53 (13 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2227 (Rfree = 0.000) for 5673 atoms. Found 21 (27 requested) and removed 37 (13 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 5634 atoms. Found 18 (26 requested) and removed 33 (13 requested) atoms. Cycle 15: After refmac, R = 0.2016 (Rfree = 0.000) for 5606 atoms. Found 16 (26 requested) and removed 40 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 5830 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5848 seeds are put forward Round 1: 340 peptides, 67 chains. Longest chain 9 peptides. Score 0.297 Round 2: 396 peptides, 63 chains. Longest chain 20 peptides. Score 0.414 Round 3: 404 peptides, 62 chains. Longest chain 16 peptides. Score 0.432 Round 4: 394 peptides, 60 chains. Longest chain 23 peptides. Score 0.431 Round 5: 393 peptides, 55 chains. Longest chain 20 peptides. Score 0.462 Taking the results from Round 5 Chains 57, Residues 338, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 13854 restraints for refining 6059 atoms. 12502 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2375 (Rfree = 0.000) for 6059 atoms. Found 26 (28 requested) and removed 43 (14 requested) atoms. Cycle 17: After refmac, R = 0.2246 (Rfree = 0.000) for 5992 atoms. Found 19 (28 requested) and removed 30 (14 requested) atoms. Cycle 18: After refmac, R = 0.2173 (Rfree = 0.000) for 5917 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 19: After refmac, R = 0.2049 (Rfree = 0.000) for 5886 atoms. Found 21 (28 requested) and removed 25 (14 requested) atoms. Cycle 20: After refmac, R = 0.2076 (Rfree = 0.000) for 5860 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.41 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6051 seeds are put forward Round 1: 322 peptides, 65 chains. Longest chain 9 peptides. Score 0.281 Round 2: 394 peptides, 63 chains. Longest chain 15 peptides. Score 0.411 Round 3: 379 peptides, 62 chains. Longest chain 14 peptides. Score 0.395 Round 4: 413 peptides, 63 chains. Longest chain 14 peptides. Score 0.439 Round 5: 403 peptides, 63 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 4 Chains 64, Residues 350, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14311 restraints for refining 6140 atoms. 12934 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2247 (Rfree = 0.000) for 6140 atoms. Found 28 (29 requested) and removed 51 (14 requested) atoms. Cycle 22: After refmac, R = 0.2130 (Rfree = 0.000) for 6058 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 23: After refmac, R = 0.2040 (Rfree = 0.000) for 6020 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 24: After refmac, R = 0.1958 (Rfree = 0.000) for 5991 atoms. Found 22 (28 requested) and removed 26 (14 requested) atoms. Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 5950 atoms. Found 24 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 6201 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6220 seeds are put forward Round 1: 322 peptides, 66 chains. Longest chain 8 peptides. Score 0.274 Round 2: 367 peptides, 63 chains. Longest chain 11 peptides. Score 0.369 Round 3: 389 peptides, 64 chains. Longest chain 13 peptides. Score 0.397 Round 4: 379 peptides, 64 chains. Longest chain 15 peptides. Score 0.381 Round 5: 373 peptides, 57 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 5 Chains 57, Residues 316, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14665 restraints for refining 6140 atoms. 13458 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2015 (Rfree = 0.000) for 6140 atoms. Found 26 (29 requested) and removed 52 (14 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 6081 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 28: After refmac, R = 0.1932 (Rfree = 0.000) for 6052 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 29: After refmac, R = 0.1478 (Rfree = 0.000) for 6032 atoms. Found 2 (28 requested) and removed 17 (14 requested) atoms. Cycle 30: After refmac, R = 0.1374 (Rfree = 0.000) for 6002 atoms. Found 4 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.44 Search for helices and strands: 0 residues in 0 chains, 6186 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6198 seeds are put forward Round 1: 289 peptides, 60 chains. Longest chain 11 peptides. Score 0.260 Round 2: 339 peptides, 62 chains. Longest chain 10 peptides. Score 0.331 Round 3: 351 peptides, 62 chains. Longest chain 12 peptides. Score 0.351 Round 4: 369 peptides, 57 chains. Longest chain 18 peptides. Score 0.413 Round 5: 372 peptides, 60 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 4 Chains 57, Residues 312, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14501 restraints for refining 6141 atoms. 13310 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1872 (Rfree = 0.000) for 6141 atoms. Found 26 (29 requested) and removed 21 (14 requested) atoms. Cycle 32: After refmac, R = 0.2064 (Rfree = 0.000) for 6094 atoms. Found 29 (29 requested) and removed 41 (14 requested) atoms. Cycle 33: After refmac, R = 0.1912 (Rfree = 0.000) for 6053 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1502 (Rfree = 0.000) for 6030 atoms. Found 5 (28 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1360 (Rfree = 0.000) for 6000 atoms. Found 9 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 6205 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 6233 seeds are put forward Round 1: 304 peptides, 62 chains. Longest chain 9 peptides. Score 0.272 Round 2: 383 peptides, 67 chains. Longest chain 14 peptides. Score 0.367 Round 3: 362 peptides, 61 chains. Longest chain 15 peptides. Score 0.375 Round 4: 350 peptides, 58 chains. Longest chain 15 peptides. Score 0.377 Round 5: 385 peptides, 61 chains. Longest chain 15 peptides. Score 0.411 Taking the results from Round 5 Chains 61, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14323 restraints for refining 6139 atoms. 13088 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1948 (Rfree = 0.000) for 6139 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 37: After refmac, R = 0.1634 (Rfree = 0.000) for 6110 atoms. Found 12 (29 requested) and removed 19 (14 requested) atoms. Cycle 38: After refmac, R = 0.1680 (Rfree = 0.000) for 6081 atoms. Found 20 (28 requested) and removed 26 (14 requested) atoms. Cycle 39: After refmac, R = 0.1748 (Rfree = 0.000) for 6070 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 40: After refmac, R = 0.1886 (Rfree = 0.000) for 6066 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 6261 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6280 seeds are put forward Round 1: 300 peptides, 65 chains. Longest chain 10 peptides. Score 0.242 Round 2: 321 peptides, 62 chains. Longest chain 10 peptides. Score 0.301 Round 3: 339 peptides, 63 chains. Longest chain 10 peptides. Score 0.324 Round 4: 349 peptides, 61 chains. Longest chain 12 peptides. Score 0.355 Round 5: 350 peptides, 60 chains. Longest chain 12 peptides. Score 0.363 Taking the results from Round 5 Chains 60, Residues 290, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14673 restraints for refining 6141 atoms. 13573 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 6141 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 42: After refmac, R = 0.2042 (Rfree = 0.000) for 6124 atoms. Found 29 (29 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.2038 (Rfree = 0.000) for 6102 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 44: After refmac, R = 0.1856 (Rfree = 0.000) for 6087 atoms. Found 27 (28 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.1999 (Rfree = 0.000) for 6080 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.41 Search for helices and strands: 0 residues in 0 chains, 6287 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6299 seeds are put forward Round 1: 255 peptides, 57 chains. Longest chain 8 peptides. Score 0.220 Round 2: 294 peptides, 55 chains. Longest chain 10 peptides. Score 0.306 Round 3: 315 peptides, 56 chains. Longest chain 13 peptides. Score 0.335 Round 4: 301 peptides, 57 chains. Longest chain 14 peptides. Score 0.304 Round 5: 309 peptides, 53 chains. Longest chain 16 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 256, 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 14892 restraints for refining 6140 atoms. 13921 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2159 (Rfree = 0.000) for 6140 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 6089 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2077 (Rfree = 0.000) for 6057 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2035 (Rfree = 0.000) for 6021 atoms. TimeTaking 68.28