Mon 24 Dec 00:44:30 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 1vl4-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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/1vl4-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 00:44:34 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/1vl4-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 688 and 0 Target number of residues in the AU: 688 Target solvent content: 0.6382 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-4.0-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.70 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: 79.862 4.000 Wilson plot Bfac: 70.96 9072 reflections ( 99.17 % complete ) and 0 restraints for refining 7946 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3142 (Rfree = 0.000) for 7946 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 8075 seeds are put forward NCS extension: 0 residues added, 8075 seeds are put forward Round 1: 339 peptides, 65 chains. Longest chain 14 peptides. Score 0.315 Round 2: 451 peptides, 69 chains. Longest chain 14 peptides. Score 0.465 Round 3: 508 peptides, 66 chains. Longest chain 25 peptides. Score 0.560 Round 4: 510 peptides, 69 chains. Longest chain 16 peptides. Score 0.545 Round 5: 497 peptides, 65 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 3 Chains 68, Residues 442, Estimated correctness of the model 0.0 % 7 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14028 restraints for refining 6459 atoms. 12082 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2720 (Rfree = 0.000) for 6459 atoms. Found 25 (30 requested) and removed 59 (15 requested) atoms. Cycle 2: After refmac, R = 0.2554 (Rfree = 0.000) for 6277 atoms. Found 30 (30 requested) and removed 43 (15 requested) atoms. Cycle 3: After refmac, R = 0.2416 (Rfree = 0.000) for 6161 atoms. Found 19 (29 requested) and removed 30 (14 requested) atoms. Cycle 4: After refmac, R = 0.2204 (Rfree = 0.000) for 6091 atoms. Found 12 (29 requested) and removed 26 (14 requested) atoms. Cycle 5: After refmac, R = 0.2158 (Rfree = 0.000) for 6033 atoms. Found 13 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 6206 seeds are put forward NCS extension: 38 residues added (0 deleted due to clashes), 6244 seeds are put forward Round 1: 404 peptides, 73 chains. Longest chain 10 peptides. Score 0.366 Round 2: 475 peptides, 67 chains. Longest chain 19 peptides. Score 0.511 Round 3: 485 peptides, 68 chains. Longest chain 15 peptides. Score 0.518 Round 4: 499 peptides, 65 chains. Longest chain 24 peptides. Score 0.554 Round 5: 497 peptides, 66 chains. Longest chain 22 peptides. Score 0.546 Taking the results from Round 4 Chains 71, Residues 434, Estimated correctness of the model 0.0 % 11 chains (88 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 13353 restraints for refining 6271 atoms. 11374 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2413 (Rfree = 0.000) for 6271 atoms. Found 27 (29 requested) and removed 72 (14 requested) atoms. Cycle 7: After refmac, R = 0.2102 (Rfree = 0.000) for 6148 atoms. Found 15 (29 requested) and removed 46 (14 requested) atoms. Cycle 8: After refmac, R = 0.1998 (Rfree = 0.000) for 6085 atoms. Found 8 (29 requested) and removed 24 (14 requested) atoms. Cycle 9: After refmac, R = 0.1967 (Rfree = 0.000) for 6062 atoms. Found 5 (28 requested) and removed 24 (14 requested) atoms. Cycle 10: After refmac, R = 0.1963 (Rfree = 0.000) for 6038 atoms. Found 2 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 6191 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6208 seeds are put forward Round 1: 420 peptides, 71 chains. Longest chain 15 peptides. Score 0.405 Round 2: 459 peptides, 67 chains. Longest chain 24 peptides. Score 0.489 Round 3: 474 peptides, 65 chains. Longest chain 19 peptides. Score 0.522 Round 4: 471 peptides, 66 chains. Longest chain 19 peptides. Score 0.512 Round 5: 493 peptides, 66 chains. Longest chain 18 peptides. Score 0.541 Taking the results from Round 5 Chains 69, Residues 427, Estimated correctness of the model 0.0 % 7 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14266 restraints for refining 6459 atoms. 12428 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2290 (Rfree = 0.000) for 6459 atoms. Found 21 (30 requested) and removed 43 (15 requested) atoms. Cycle 12: After refmac, R = 0.2159 (Rfree = 0.000) for 6386 atoms. Found 20 (30 requested) and removed 36 (15 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 6348 atoms. Found 8 (30 requested) and removed 33 (15 requested) atoms. Cycle 14: After refmac, R = 0.2015 (Rfree = 0.000) for 6306 atoms. Found 9 (30 requested) and removed 24 (15 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 6283 atoms. Found 7 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6437 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6450 seeds are put forward Round 1: 381 peptides, 71 chains. Longest chain 13 peptides. Score 0.342 Round 2: 442 peptides, 67 chains. Longest chain 26 peptides. Score 0.465 Round 3: 477 peptides, 72 chains. Longest chain 19 peptides. Score 0.483 Round 4: 475 peptides, 68 chains. Longest chain 20 peptides. Score 0.505 Round 5: 464 peptides, 65 chains. Longest chain 19 peptides. Score 0.508 Taking the results from Round 5 Chains 67, Residues 399, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14740 restraints for refining 6458 atoms. 13062 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2246 (Rfree = 0.000) for 6458 atoms. Found 15 (30 requested) and removed 45 (15 requested) atoms. Cycle 17: After refmac, R = 0.2102 (Rfree = 0.000) for 6375 atoms. Found 11 (30 requested) and removed 35 (15 requested) atoms. Cycle 18: After refmac, R = 0.2063 (Rfree = 0.000) for 6335 atoms. Found 10 (30 requested) and removed 52 (15 requested) atoms. Cycle 19: After refmac, R = 0.2072 (Rfree = 0.000) for 6288 atoms. Found 16 (29 requested) and removed 42 (14 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 6257 atoms. Found 11 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6413 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 6430 seeds are put forward Round 1: 370 peptides, 70 chains. Longest chain 11 peptides. Score 0.331 Round 2: 412 peptides, 65 chains. Longest chain 16 peptides. Score 0.433 Round 3: 409 peptides, 68 chains. Longest chain 17 peptides. Score 0.408 Round 4: 422 peptides, 66 chains. Longest chain 17 peptides. Score 0.442 Round 5: 419 peptides, 62 chains. Longest chain 21 peptides. Score 0.463 Taking the results from Round 5 Chains 64, Residues 357, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15061 restraints for refining 6459 atoms. 13555 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2180 (Rfree = 0.000) for 6459 atoms. Found 15 (30 requested) and removed 41 (15 requested) atoms. Cycle 22: After refmac, R = 0.2054 (Rfree = 0.000) for 6399 atoms. Found 29 (30 requested) and removed 32 (15 requested) atoms. Cycle 23: After refmac, R = 0.2120 (Rfree = 0.000) for 6379 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 24: After refmac, R = 0.1744 (Rfree = 0.000) for 6356 atoms. Found 7 (30 requested) and removed 28 (15 requested) atoms. Cycle 25: After refmac, R = 0.1685 (Rfree = 0.000) for 6316 atoms. Found 7 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 6470 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6492 seeds are put forward Round 1: 351 peptides, 71 chains. Longest chain 10 peptides. Score 0.291 Round 2: 399 peptides, 72 chains. Longest chain 15 peptides. Score 0.365 Round 3: 432 peptides, 75 chains. Longest chain 15 peptides. Score 0.397 Round 4: 410 peptides, 67 chains. Longest chain 21 peptides. Score 0.417 Round 5: 402 peptides, 66 chains. Longest chain 20 peptides. Score 0.411 Taking the results from Round 4 Chains 69, Residues 343, Estimated correctness of the model 0.0 % 7 chains (52 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15013 restraints for refining 6457 atoms. 13514 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2235 (Rfree = 0.000) for 6457 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 27: After refmac, R = 0.2102 (Rfree = 0.000) for 6407 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 28: After refmac, R = 0.2209 (Rfree = 0.000) for 6370 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 6345 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 30: After refmac, R = 0.1742 (Rfree = 0.000) for 6320 atoms. Found 12 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 6441 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6465 seeds are put forward Round 1: 309 peptides, 62 chains. Longest chain 14 peptides. Score 0.284 Round 2: 361 peptides, 68 chains. Longest chain 13 peptides. Score 0.330 Round 3: 361 peptides, 61 chains. Longest chain 16 peptides. Score 0.381 Round 4: 391 peptides, 65 chains. Longest chain 16 peptides. Score 0.401 Round 5: 354 peptides, 60 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 4 Chains 69, Residues 326, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14951 restraints for refining 6459 atoms. 13568 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2067 (Rfree = 0.000) for 6459 atoms. Found 24 (30 requested) and removed 34 (15 requested) atoms. Cycle 32: After refmac, R = 0.1971 (Rfree = 0.000) for 6420 atoms. Found 19 (30 requested) and removed 25 (15 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 6396 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 34: After refmac, R = 0.1841 (Rfree = 0.000) for 6390 atoms. Found 15 (30 requested) and removed 28 (15 requested) atoms. Cycle 35: After refmac, R = 0.1842 (Rfree = 0.000) for 6367 atoms. Found 5 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 6477 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6490 seeds are put forward Round 1: 327 peptides, 64 chains. Longest chain 11 peptides. Score 0.301 Round 2: 377 peptides, 63 chains. Longest chain 15 peptides. Score 0.392 Round 3: 357 peptides, 56 chains. Longest chain 16 peptides. Score 0.409 Round 4: 367 peptides, 59 chains. Longest chain 15 peptides. Score 0.404 Round 5: 351 peptides, 54 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 54, Residues 297, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15536 restraints for refining 6458 atoms. 14320 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2265 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 45 (15 requested) atoms. Cycle 37: After refmac, R = 0.2176 (Rfree = 0.000) for 6404 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 38: After refmac, R = 0.1783 (Rfree = 0.000) for 6374 atoms. Found 8 (30 requested) and removed 23 (15 requested) atoms. Cycle 39: After refmac, R = 0.1950 (Rfree = 0.000) for 6347 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 40: After refmac, R = 0.1736 (Rfree = 0.000) for 6339 atoms. Found 10 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 6473 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6492 seeds are put forward Round 1: 285 peptides, 60 chains. Longest chain 10 peptides. Score 0.256 Round 2: 323 peptides, 60 chains. Longest chain 15 peptides. Score 0.324 Round 3: 322 peptides, 56 chains. Longest chain 13 peptides. Score 0.352 Round 4: 332 peptides, 57 chains. Longest chain 13 peptides. Score 0.362 Round 5: 318 peptides, 54 chains. Longest chain 18 peptides. Score 0.360 Taking the results from Round 4 Chains 57, Residues 275, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15558 restraints for refining 6458 atoms. 14481 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2337 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 64 (15 requested) atoms. Cycle 42: After refmac, R = 0.2396 (Rfree = 0.000) for 6384 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 43: After refmac, R = 0.1882 (Rfree = 0.000) for 6360 atoms. Found 12 (30 requested) and removed 24 (15 requested) atoms. Cycle 44: After refmac, R = 0.2116 (Rfree = 0.000) for 6319 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 45: After refmac, R = 0.1824 (Rfree = 0.000) for 6301 atoms. Found 11 (30 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 6395 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6408 seeds are put forward Round 1: 262 peptides, 54 chains. Longest chain 10 peptides. Score 0.260 Round 2: 324 peptides, 60 chains. Longest chain 18 peptides. Score 0.326 Round 3: 330 peptides, 56 chains. Longest chain 11 peptides. Score 0.366 Round 4: 314 peptides, 55 chains. Longest chain 16 peptides. Score 0.346 Round 5: 317 peptides, 55 chains. Longest chain 13 peptides. Score 0.351 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 274, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vl4-4_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (274 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9072 reflections ( 99.17 % complete ) and 14765 restraints for refining 6280 atoms. 13652 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2349 (Rfree = 0.000) for 6280 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2287 (Rfree = 0.000) for 6236 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2272 (Rfree = 0.000) for 6201 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2152 (Rfree = 0.000) for 6170 atoms. TimeTaking 65.38