Mon 24 Dec 00:31:13 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vp4-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-parrot-mrncs ############### 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 00:31:18 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 7537 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3654 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3442 (Rfree = 0.000) for 7537 atoms. Found 35 (35 requested) and removed 66 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 7649 seeds are put forward NCS extension: 0 residues added, 7649 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 8 peptides. Score 0.256 Round 2: 320 peptides, 60 chains. Longest chain 10 peptides. Score 0.314 Round 3: 364 peptides, 60 chains. Longest chain 15 peptides. Score 0.385 Round 4: 381 peptides, 56 chains. Longest chain 16 peptides. Score 0.438 Round 5: 408 peptides, 56 chains. Longest chain 21 peptides. Score 0.476 Taking the results from Round 5 Chains 56, Residues 352, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14582 restraints for refining 6138 atoms. 13230 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2742 (Rfree = 0.000) for 6138 atoms. Found 22 (29 requested) and removed 42 (14 requested) atoms. Cycle 2: After refmac, R = 0.2573 (Rfree = 0.000) for 6008 atoms. Found 16 (29 requested) and removed 34 (14 requested) atoms. Cycle 3: After refmac, R = 0.2648 (Rfree = 0.000) for 5921 atoms. Found 23 (28 requested) and removed 21 (14 requested) atoms. Cycle 4: After refmac, R = 0.2586 (Rfree = 0.000) for 5876 atoms. Found 14 (28 requested) and removed 22 (14 requested) atoms. Cycle 5: After refmac, R = 0.2567 (Rfree = 0.000) for 5818 atoms. Found 21 (27 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.41 Search for helices and strands: 0 residues in 0 chains, 6055 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6067 seeds are put forward Round 1: 344 peptides, 66 chains. Longest chain 17 peptides. Score 0.311 Round 2: 415 peptides, 66 chains. Longest chain 16 peptides. Score 0.423 Round 3: 418 peptides, 63 chains. Longest chain 20 peptides. Score 0.446 Round 4: 444 peptides, 66 chains. Longest chain 15 peptides. Score 0.464 Round 5: 429 peptides, 62 chains. Longest chain 23 peptides. Score 0.468 Taking the results from Round 5 Chains 62, Residues 367, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 13928 restraints for refining 5932 atoms. 12500 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2503 (Rfree = 0.000) for 5932 atoms. Found 28 (28 requested) and removed 38 (14 requested) atoms. Cycle 7: After refmac, R = 0.2279 (Rfree = 0.000) for 5870 atoms. Found 26 (28 requested) and removed 34 (14 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 5829 atoms. Found 10 (27 requested) and removed 23 (13 requested) atoms. Cycle 9: After refmac, R = 0.2126 (Rfree = 0.000) for 5807 atoms. Found 7 (27 requested) and removed 20 (13 requested) atoms. Cycle 10: After refmac, R = 0.2076 (Rfree = 0.000) for 5786 atoms. Found 10 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.43 Search for helices and strands: 0 residues in 0 chains, 5977 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6002 seeds are put forward Round 1: 372 peptides, 66 chains. Longest chain 10 peptides. Score 0.357 Round 2: 414 peptides, 63 chains. Longest chain 20 peptides. Score 0.440 Round 3: 435 peptides, 66 chains. Longest chain 15 peptides. Score 0.452 Round 4: 443 peptides, 64 chains. Longest chain 20 peptides. Score 0.475 Round 5: 418 peptides, 59 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Chains 64, Residues 379, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14260 restraints for refining 6140 atoms. 12794 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2133 (Rfree = 0.000) for 6140 atoms. Found 19 (29 requested) and removed 31 (14 requested) atoms. Cycle 12: After refmac, R = 0.2168 (Rfree = 0.000) for 6094 atoms. Found 22 (29 requested) and removed 27 (14 requested) atoms. Cycle 13: After refmac, R = 0.2049 (Rfree = 0.000) for 6075 atoms. Found 15 (28 requested) and removed 21 (14 requested) atoms. Cycle 14: After refmac, R = 0.1806 (Rfree = 0.000) for 6053 atoms. Found 3 (28 requested) and removed 16 (14 requested) atoms. Cycle 15: After refmac, R = 0.1816 (Rfree = 0.000) for 6028 atoms. Found 6 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 6257 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6281 seeds are put forward Round 1: 359 peptides, 65 chains. Longest chain 14 peptides. Score 0.343 Round 2: 403 peptides, 63 chains. Longest chain 20 peptides. Score 0.424 Round 3: 431 peptides, 63 chains. Longest chain 16 peptides. Score 0.465 Round 4: 422 peptides, 59 chains. Longest chain 16 peptides. Score 0.477 Round 5: 407 peptides, 56 chains. Longest chain 23 peptides. Score 0.475 Taking the results from Round 4 Chains 62, Residues 363, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14230 restraints for refining 6140 atoms. 12744 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2119 (Rfree = 0.000) for 6140 atoms. Found 15 (29 requested) and removed 15 (14 requested) atoms. Cycle 17: After refmac, R = 0.1984 (Rfree = 0.000) for 6104 atoms. Found 12 (29 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.1953 (Rfree = 0.000) for 6085 atoms. Found 8 (28 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.1951 (Rfree = 0.000) for 6060 atoms. Found 3 (28 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.1939 (Rfree = 0.000) for 6040 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.42 Search for helices and strands: 0 residues in 0 chains, 6240 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6255 seeds are put forward Round 1: 360 peptides, 63 chains. Longest chain 13 peptides. Score 0.358 Round 2: 395 peptides, 62 chains. Longest chain 17 peptides. Score 0.419 Round 3: 394 peptides, 61 chains. Longest chain 19 peptides. Score 0.424 Round 4: 393 peptides, 63 chains. Longest chain 13 peptides. Score 0.409 Round 5: 408 peptides, 62 chains. Longest chain 22 peptides. Score 0.438 Taking the results from Round 5 Chains 62, Residues 346, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14563 restraints for refining 6139 atoms. 13241 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2098 (Rfree = 0.000) for 6139 atoms. Found 13 (29 requested) and removed 50 (14 requested) atoms. Cycle 22: After refmac, R = 0.1982 (Rfree = 0.000) for 6083 atoms. Found 7 (28 requested) and removed 22 (14 requested) atoms. Cycle 23: After refmac, R = 0.1942 (Rfree = 0.000) for 6059 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.1931 (Rfree = 0.000) for 6049 atoms. Found 2 (28 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.1924 (Rfree = 0.000) for 6036 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.46 Search for helices and strands: 0 residues in 0 chains, 6217 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6245 seeds are put forward Round 1: 315 peptides, 62 chains. Longest chain 13 peptides. Score 0.291 Round 2: 354 peptides, 59 chains. Longest chain 12 peptides. Score 0.377 Round 3: 384 peptides, 59 chains. Longest chain 15 peptides. Score 0.423 Round 4: 380 peptides, 56 chains. Longest chain 16 peptides. Score 0.436 Round 5: 375 peptides, 57 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 4 Chains 56, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14955 restraints for refining 6140 atoms. 13715 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 6140 atoms. Found 24 (29 requested) and removed 80 (14 requested) atoms. Cycle 27: After refmac, R = 0.2208 (Rfree = 0.000) for 6072 atoms. Found 13 (28 requested) and removed 79 (14 requested) atoms. Cycle 28: After refmac, R = 0.2141 (Rfree = 0.000) for 5993 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 5980 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2102 (Rfree = 0.000) for 5970 atoms. Found 1 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.45 Search for helices and strands: 0 residues in 0 chains, 6152 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6167 seeds are put forward Round 1: 321 peptides, 62 chains. Longest chain 11 peptides. Score 0.301 Round 2: 361 peptides, 58 chains. Longest chain 11 peptides. Score 0.394 Round 3: 375 peptides, 63 chains. Longest chain 12 peptides. Score 0.382 Round 4: 371 peptides, 56 chains. Longest chain 14 peptides. Score 0.423 Round 5: 354 peptides, 56 chains. Longest chain 17 peptides. Score 0.397 Taking the results from Round 4 Chains 57, Residues 315, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14679 restraints for refining 6141 atoms. 13428 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2385 (Rfree = 0.000) for 6141 atoms. Found 22 (29 requested) and removed 18 (14 requested) atoms. Cycle 32: After refmac, R = 0.2260 (Rfree = 0.000) for 6128 atoms. Found 10 (29 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2228 (Rfree = 0.000) for 6118 atoms. Found 6 (29 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2206 (Rfree = 0.000) for 6108 atoms. Found 2 (29 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2194 (Rfree = 0.000) for 6094 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.46 Search for helices and strands: 0 residues in 0 chains, 6246 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6261 seeds are put forward Round 1: 292 peptides, 60 chains. Longest chain 10 peptides. Score 0.265 Round 2: 314 peptides, 53 chains. Longest chain 13 peptides. Score 0.355 Round 3: 335 peptides, 56 chains. Longest chain 11 peptides. Score 0.367 Round 4: 352 peptides, 56 chains. Longest chain 17 peptides. Score 0.394 Round 5: 355 peptides, 53 chains. Longest chain 23 peptides. Score 0.419 Taking the results from Round 5 Chains 53, Residues 302, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14944 restraints for refining 6140 atoms. 13780 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 6140 atoms. Found 18 (29 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.2242 (Rfree = 0.000) for 6124 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. Cycle 38: After refmac, R = 0.2196 (Rfree = 0.000) for 6113 atoms. Found 3 (29 requested) and removed 19 (14 requested) atoms. Cycle 39: After refmac, R = 0.2174 (Rfree = 0.000) for 6096 atoms. Found 6 (28 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2163 (Rfree = 0.000) for 6087 atoms. Found 1 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.48 Search for helices and strands: 0 residues in 0 chains, 6213 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6240 seeds are put forward Round 1: 271 peptides, 55 chains. Longest chain 10 peptides. Score 0.266 Round 2: 319 peptides, 60 chains. Longest chain 10 peptides. Score 0.312 Round 3: 352 peptides, 59 chains. Longest chain 13 peptides. Score 0.373 Round 4: 348 peptides, 57 chains. Longest chain 13 peptides. Score 0.381 Round 5: 342 peptides, 59 chains. Longest chain 15 peptides. Score 0.357 Taking the results from Round 4 Chains 58, Residues 291, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9154 reflections ( 99.65 % complete ) and 14544 restraints for refining 6140 atoms. 13356 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2340 (Rfree = 0.000) for 6140 atoms. Found 19 (29 requested) and removed 33 (14 requested) atoms. Cycle 42: After refmac, R = 0.2319 (Rfree = 0.000) for 6096 atoms. Found 10 (29 requested) and removed 18 (14 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 6085 atoms. Found 6 (28 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2264 (Rfree = 0.000) for 6074 atoms. Found 9 (28 requested) and removed 27 (14 requested) atoms. Cycle 45: After refmac, R = 0.2235 (Rfree = 0.000) for 6054 atoms. Found 2 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.46 Search for helices and strands: 0 residues in 0 chains, 6199 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6212 seeds are put forward Round 1: 230 peptides, 48 chains. Longest chain 12 peptides. Score 0.245 Round 2: 291 peptides, 48 chains. Longest chain 15 peptides. Score 0.354 Round 3: 288 peptides, 50 chains. Longest chain 14 peptides. Score 0.334 Round 4: 293 peptides, 47 chains. Longest chain 14 peptides. Score 0.364 Round 5: 306 peptides, 52 chains. Longest chain 15 peptides. Score 0.349 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 246, 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 15309 restraints for refining 6140 atoms. 14372 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2241 (Rfree = 0.000) for 6140 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2159 (Rfree = 0.000) for 6109 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2144 (Rfree = 0.000) for 6087 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2148 (Rfree = 0.000) for 6067 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 77.17