null Sun 23 Dec 22:23:10 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 1vqr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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/1vqr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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 22:23:20 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/1vqr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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 802 and 0 Target number of residues in the AU: 802 Target solvent content: 0.6539 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 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: 83.418 4.000 Wilson plot Bfac: 80.47 9486 reflections ( 90.22 % complete ) and 0 restraints for refining 10466 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3737 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3359 (Rfree = 0.000) for 10466 atoms. Found 45 (49 requested) and removed 235 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 10352 seeds are put forward NCS extension: 0 residues added, 10352 seeds are put forward Round 1: 188 peptides, 45 chains. Longest chain 5 peptides. Score 0.183 Round 2: 249 peptides, 57 chains. Longest chain 7 peptides. Score 0.205 Round 3: 284 peptides, 62 chains. Longest chain 7 peptides. Score 0.229 Round 4: 309 peptides, 63 chains. Longest chain 8 peptides. Score 0.262 Round 5: 303 peptides, 64 chains. Longest chain 8 peptides. Score 0.246 Taking the results from Round 4 Chains 63, Residues 246, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 22180 restraints for refining 8577 atoms. 21242 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2873 (Rfree = 0.000) for 8577 atoms. Found 21 (40 requested) and removed 82 (20 requested) atoms. Cycle 2: After refmac, R = 0.2622 (Rfree = 0.000) for 8376 atoms. Found 38 (40 requested) and removed 76 (20 requested) atoms. Cycle 3: After refmac, R = 0.2545 (Rfree = 0.000) for 8266 atoms. Found 30 (39 requested) and removed 58 (19 requested) atoms. Cycle 4: After refmac, R = 0.2062 (Rfree = 0.000) for 8163 atoms. Found 10 (39 requested) and removed 36 (19 requested) atoms. Cycle 5: After refmac, R = 0.1936 (Rfree = 0.000) for 8110 atoms. Found 6 (38 requested) and removed 34 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 8210 seeds are put forward NCS extension: 0 residues added, 8210 seeds are put forward Round 1: 267 peptides, 62 chains. Longest chain 6 peptides. Score 0.200 Round 2: 354 peptides, 73 chains. Longest chain 9 peptides. Score 0.266 Round 3: 364 peptides, 73 chains. Longest chain 11 peptides. Score 0.282 Round 4: 352 peptides, 69 chains. Longest chain 9 peptides. Score 0.289 Round 5: 377 peptides, 72 chains. Longest chain 11 peptides. Score 0.307 Taking the results from Round 5 Chains 72, Residues 305, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 17778 restraints for refining 7446 atoms. 16630 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2513 (Rfree = 0.000) for 7446 atoms. Found 35 (35 requested) and removed 50 (17 requested) atoms. Cycle 7: After refmac, R = 0.2386 (Rfree = 0.000) for 7366 atoms. Found 30 (35 requested) and removed 49 (17 requested) atoms. Cycle 8: After refmac, R = 0.2344 (Rfree = 0.000) for 7296 atoms. Found 25 (34 requested) and removed 42 (17 requested) atoms. Cycle 9: After refmac, R = 0.2339 (Rfree = 0.000) for 7241 atoms. Found 26 (34 requested) and removed 34 (17 requested) atoms. Cycle 10: After refmac, R = 0.2261 (Rfree = 0.000) for 7196 atoms. Found 28 (34 requested) and removed 39 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 7318 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7330 seeds are put forward Round 1: 334 peptides, 70 chains. Longest chain 9 peptides. Score 0.255 Round 2: 349 peptides, 65 chains. Longest chain 14 peptides. Score 0.310 Round 3: 345 peptides, 62 chains. Longest chain 11 peptides. Score 0.323 Round 4: 377 peptides, 68 chains. Longest chain 11 peptides. Score 0.332 Round 5: 362 peptides, 65 chains. Longest chain 11 peptides. Score 0.329 Taking the results from Round 4 Chains 68, Residues 309, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 17030 restraints for refining 7295 atoms. 15862 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 7295 atoms. Found 34 (34 requested) and removed 87 (17 requested) atoms. Cycle 12: After refmac, R = 0.2337 (Rfree = 0.000) for 7202 atoms. Found 34 (34 requested) and removed 53 (17 requested) atoms. Cycle 13: After refmac, R = 0.1910 (Rfree = 0.000) for 7159 atoms. Found 10 (34 requested) and removed 26 (17 requested) atoms. Cycle 14: After refmac, R = 0.1825 (Rfree = 0.000) for 7129 atoms. Found 5 (33 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.1790 (Rfree = 0.000) for 7109 atoms. Found 6 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 7240 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7254 seeds are put forward Round 1: 351 peptides, 78 chains. Longest chain 7 peptides. Score 0.230 Round 2: 371 peptides, 70 chains. Longest chain 12 peptides. Score 0.311 Round 3: 401 peptides, 80 chains. Longest chain 9 peptides. Score 0.292 Round 4: 412 peptides, 74 chains. Longest chain 12 peptides. Score 0.345 Round 5: 423 peptides, 81 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 4 Chains 74, Residues 338, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 17189 restraints for refining 7409 atoms. 15911 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2353 (Rfree = 0.000) for 7409 atoms. Found 34 (35 requested) and removed 56 (17 requested) atoms. Cycle 17: After refmac, R = 0.2302 (Rfree = 0.000) for 7348 atoms. Found 35 (35 requested) and removed 41 (17 requested) atoms. Cycle 18: After refmac, R = 0.2156 (Rfree = 0.000) for 7318 atoms. Found 31 (34 requested) and removed 39 (17 requested) atoms. Cycle 19: After refmac, R = 0.1824 (Rfree = 0.000) for 7292 atoms. Found 11 (34 requested) and removed 34 (17 requested) atoms. Cycle 20: After refmac, R = 0.1814 (Rfree = 0.000) for 7254 atoms. Found 7 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 7355 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7369 seeds are put forward Round 1: 307 peptides, 67 chains. Longest chain 8 peptides. Score 0.232 Round 2: 362 peptides, 69 chains. Longest chain 10 peptides. Score 0.304 Round 3: 386 peptides, 71 chains. Longest chain 12 peptides. Score 0.326 Round 4: 384 peptides, 69 chains. Longest chain 10 peptides. Score 0.336 Round 5: 389 peptides, 66 chains. Longest chain 14 peptides. Score 0.361 Taking the results from Round 5 Chains 67, Residues 323, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18092 restraints for refining 7650 atoms. 16833 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2277 (Rfree = 0.000) for 7650 atoms. Found 34 (36 requested) and removed 80 (18 requested) atoms. Cycle 22: After refmac, R = 0.2127 (Rfree = 0.000) for 7573 atoms. Found 27 (36 requested) and removed 42 (18 requested) atoms. Cycle 23: After refmac, R = 0.1849 (Rfree = 0.000) for 7534 atoms. Found 8 (35 requested) and removed 41 (17 requested) atoms. Cycle 24: After refmac, R = 0.1759 (Rfree = 0.000) for 7492 atoms. Found 8 (35 requested) and removed 27 (17 requested) atoms. Cycle 25: After refmac, R = 0.1771 (Rfree = 0.000) for 7467 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 7591 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7609 seeds are put forward Round 1: 332 peptides, 72 chains. Longest chain 10 peptides. Score 0.239 Round 2: 382 peptides, 72 chains. Longest chain 12 peptides. Score 0.314 Round 3: 379 peptides, 69 chains. Longest chain 12 peptides. Score 0.329 Round 4: 398 peptides, 72 chains. Longest chain 11 peptides. Score 0.337 Round 5: 386 peptides, 69 chains. Longest chain 12 peptides. Score 0.338 Taking the results from Round 5 Chains 69, Residues 317, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18573 restraints for refining 7819 atoms. 17374 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2387 (Rfree = 0.000) for 7819 atoms. Found 37 (37 requested) and removed 70 (18 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 7748 atoms. Found 31 (36 requested) and removed 42 (18 requested) atoms. Cycle 28: After refmac, R = 0.2282 (Rfree = 0.000) for 7701 atoms. Found 36 (36 requested) and removed 46 (18 requested) atoms. Cycle 29: After refmac, R = 0.1670 (Rfree = 0.000) for 7659 atoms. Found 11 (36 requested) and removed 27 (18 requested) atoms. Cycle 30: After refmac, R = 0.1642 (Rfree = 0.000) for 7622 atoms. Found 5 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 7764 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7777 seeds are put forward Round 1: 284 peptides, 61 chains. Longest chain 11 peptides. Score 0.236 Round 2: 300 peptides, 57 chains. Longest chain 11 peptides. Score 0.289 Round 3: 319 peptides, 60 chains. Longest chain 9 peptides. Score 0.298 Round 4: 304 peptides, 58 chains. Longest chain 11 peptides. Score 0.288 Round 5: 309 peptides, 58 chains. Longest chain 11 peptides. Score 0.296 Taking the results from Round 3 Chains 60, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 17980 restraints for refining 7571 atoms. 17004 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2165 (Rfree = 0.000) for 7571 atoms. Found 35 (35 requested) and removed 57 (17 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 7522 atoms. Found 29 (35 requested) and removed 39 (17 requested) atoms. Cycle 33: After refmac, R = 0.2122 (Rfree = 0.000) for 7492 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. Cycle 34: After refmac, R = 0.1614 (Rfree = 0.000) for 7479 atoms. Found 8 (35 requested) and removed 25 (17 requested) atoms. Cycle 35: After refmac, R = 0.1548 (Rfree = 0.000) for 7451 atoms. Found 5 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 7549 seeds are put forward NCS extension: 0 residues added, 7549 seeds are put forward Round 1: 276 peptides, 60 chains. Longest chain 12 peptides. Score 0.230 Round 2: 324 peptides, 62 chains. Longest chain 13 peptides. Score 0.292 Round 3: 313 peptides, 58 chains. Longest chain 11 peptides. Score 0.302 Round 4: 311 peptides, 57 chains. Longest chain 12 peptides. Score 0.305 Round 5: 302 peptides, 54 chains. Longest chain 13 peptides. Score 0.312 Taking the results from Round 5 Chains 54, Residues 248, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18175 restraints for refining 7604 atoms. 17237 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2152 (Rfree = 0.000) for 7604 atoms. Found 30 (36 requested) and removed 69 (18 requested) atoms. Cycle 37: After refmac, R = 0.2091 (Rfree = 0.000) for 7542 atoms. Found 30 (35 requested) and removed 43 (17 requested) atoms. Cycle 38: After refmac, R = 0.2096 (Rfree = 0.000) for 7514 atoms. Found 35 (35 requested) and removed 23 (17 requested) atoms. Cycle 39: After refmac, R = 0.2157 (Rfree = 0.000) for 7502 atoms. Found 35 (35 requested) and removed 35 (17 requested) atoms. Cycle 40: After refmac, R = 0.1693 (Rfree = 0.000) for 7493 atoms. Found 11 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 7625 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7639 seeds are put forward Round 1: 241 peptides, 54 chains. Longest chain 7 peptides. Score 0.213 Round 2: 274 peptides, 54 chains. Longest chain 10 peptides. Score 0.268 Round 3: 266 peptides, 54 chains. Longest chain 9 peptides. Score 0.255 Round 4: 283 peptides, 57 chains. Longest chain 10 peptides. Score 0.262 Round 5: 280 peptides, 53 chains. Longest chain 10 peptides. Score 0.285 Taking the results from Round 5 Chains 53, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 17544 restraints for refining 7493 atoms. 16689 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2248 (Rfree = 0.000) for 7493 atoms. Found 28 (35 requested) and removed 43 (17 requested) atoms. Cycle 42: After refmac, R = 0.2143 (Rfree = 0.000) for 7463 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 43: After refmac, R = 0.2060 (Rfree = 0.000) for 7439 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 44: After refmac, R = 0.2012 (Rfree = 0.000) for 7432 atoms. Found 34 (35 requested) and removed 34 (17 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 7418 atoms. Found 26 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 7583 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7595 seeds are put forward Round 1: 222 peptides, 49 chains. Longest chain 7 peptides. Score 0.216 Round 2: 253 peptides, 52 chains. Longest chain 10 peptides. Score 0.248 Round 3: 265 peptides, 51 chains. Longest chain 11 peptides. Score 0.275 Round 4: 253 peptides, 48 chains. Longest chain 13 peptides. Score 0.276 Round 5: 266 peptides, 50 chains. Longest chain 10 peptides. Score 0.283 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 216, 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 1vqr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9486 reflections ( 90.22 % complete ) and 17621 restraints for refining 7505 atoms. 16807 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2327 (Rfree = 0.000) for 7505 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2209 (Rfree = 0.000) for 7469 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1837 (Rfree = 0.000) for 7435 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1788 (Rfree = 0.000) for 7408 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:56:57 GMT 2018 Job finished. TimeTaking 93.79 Used memory is bytes: 3251952