Mon 24 Dec 00:58:35 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 1vr0-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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/1vr0-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 00:58:40 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/1vr0-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6461 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.8-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.800 Wilson plot Bfac: 75.70 7656 reflections ( 99.57 % complete ) and 0 restraints for refining 6530 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3225 (Rfree = 0.000) for 6530 atoms. Found 35 (35 requested) and removed 67 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 6632 seeds are put forward NCS extension: 0 residues added, 6632 seeds are put forward Round 1: 265 peptides, 54 chains. Longest chain 9 peptides. Score 0.293 Round 2: 343 peptides, 55 chains. Longest chain 13 peptides. Score 0.457 Round 3: 377 peptides, 50 chains. Longest chain 24 peptides. Score 0.563 Round 4: 369 peptides, 55 chains. Longest chain 18 peptides. Score 0.508 Round 5: 387 peptides, 55 chains. Longest chain 25 peptides. Score 0.542 Taking the results from Round 3 Chains 50, Residues 327, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12547 restraints for refining 5361 atoms. 11289 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2509 (Rfree = 0.000) for 5361 atoms. Found 20 (29 requested) and removed 48 (14 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 5247 atoms. Found 22 (29 requested) and removed 31 (14 requested) atoms. Cycle 3: After refmac, R = 0.2227 (Rfree = 0.000) for 5196 atoms. Found 25 (28 requested) and removed 28 (14 requested) atoms. Cycle 4: After refmac, R = 0.2122 (Rfree = 0.000) for 5170 atoms. Found 22 (28 requested) and removed 26 (14 requested) atoms. Cycle 5: After refmac, R = 0.2080 (Rfree = 0.000) for 5141 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5347 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 5378 seeds are put forward Round 1: 310 peptides, 58 chains. Longest chain 13 peptides. Score 0.359 Round 2: 354 peptides, 55 chains. Longest chain 17 peptides. Score 0.479 Round 3: 351 peptides, 52 chains. Longest chain 21 peptides. Score 0.499 Round 4: 371 peptides, 50 chains. Longest chain 18 peptides. Score 0.553 Round 5: 378 peptides, 53 chains. Longest chain 21 peptides. Score 0.541 Taking the results from Round 4 Chains 50, Residues 321, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12243 restraints for refining 5237 atoms. 11009 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2233 (Rfree = 0.000) for 5237 atoms. Found 27 (28 requested) and removed 52 (14 requested) atoms. Cycle 7: After refmac, R = 0.1958 (Rfree = 0.000) for 5171 atoms. Found 26 (28 requested) and removed 36 (14 requested) atoms. Cycle 8: After refmac, R = 0.2058 (Rfree = 0.000) for 5143 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 9: After refmac, R = 0.1824 (Rfree = 0.000) for 5129 atoms. Found 24 (28 requested) and removed 30 (14 requested) atoms. Cycle 10: After refmac, R = 0.1411 (Rfree = 0.000) for 5116 atoms. Found 6 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5341 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5359 seeds are put forward Round 1: 322 peptides, 61 chains. Longest chain 10 peptides. Score 0.357 Round 2: 381 peptides, 55 chains. Longest chain 22 peptides. Score 0.531 Round 3: 371 peptides, 53 chains. Longest chain 20 peptides. Score 0.529 Round 4: 384 peptides, 53 chains. Longest chain 18 peptides. Score 0.552 Round 5: 383 peptides, 51 chains. Longest chain 20 peptides. Score 0.566 Taking the results from Round 5 Chains 51, Residues 332, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12526 restraints for refining 5359 atoms. 11249 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1938 (Rfree = 0.000) for 5359 atoms. Found 20 (29 requested) and removed 45 (14 requested) atoms. Cycle 12: After refmac, R = 0.1825 (Rfree = 0.000) for 5297 atoms. Found 15 (29 requested) and removed 34 (14 requested) atoms. Cycle 13: After refmac, R = 0.1864 (Rfree = 0.000) for 5261 atoms. Found 26 (29 requested) and removed 31 (14 requested) atoms. Cycle 14: After refmac, R = 0.1743 (Rfree = 0.000) for 5249 atoms. Found 23 (28 requested) and removed 23 (14 requested) atoms. Cycle 15: After refmac, R = 0.1769 (Rfree = 0.000) for 5240 atoms. Found 27 (28 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5436 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 5455 seeds are put forward Round 1: 330 peptides, 61 chains. Longest chain 11 peptides. Score 0.375 Round 2: 342 peptides, 51 chains. Longest chain 15 peptides. Score 0.490 Round 3: 368 peptides, 54 chains. Longest chain 19 peptides. Score 0.515 Round 4: 352 peptides, 52 chains. Longest chain 18 peptides. Score 0.501 Round 5: 369 peptides, 52 chains. Longest chain 26 peptides. Score 0.533 Taking the results from Round 5 Chains 52, Residues 317, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12510 restraints for refining 5362 atoms. 11294 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1905 (Rfree = 0.000) for 5362 atoms. Found 9 (29 requested) and removed 33 (14 requested) atoms. Cycle 17: After refmac, R = 0.1892 (Rfree = 0.000) for 5309 atoms. Found 23 (29 requested) and removed 30 (14 requested) atoms. Cycle 18: After refmac, R = 0.1906 (Rfree = 0.000) for 5284 atoms. Found 25 (29 requested) and removed 31 (14 requested) atoms. Cycle 19: After refmac, R = 0.1710 (Rfree = 0.000) for 5266 atoms. Found 14 (29 requested) and removed 24 (14 requested) atoms. Cycle 20: After refmac, R = 0.1801 (Rfree = 0.000) for 5251 atoms. Found 24 (28 requested) and removed 32 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 5450 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 5481 seeds are put forward Round 1: 280 peptides, 52 chains. Longest chain 14 peptides. Score 0.348 Round 2: 328 peptides, 47 chains. Longest chain 21 peptides. Score 0.497 Round 3: 330 peptides, 50 chains. Longest chain 15 peptides. Score 0.475 Round 4: 327 peptides, 48 chains. Longest chain 17 peptides. Score 0.487 Round 5: 328 peptides, 47 chains. Longest chain 16 peptides. Score 0.497 Taking the results from Round 5 Chains 47, Residues 281, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12813 restraints for refining 5360 atoms. 11736 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2107 (Rfree = 0.000) for 5360 atoms. Found 24 (29 requested) and removed 35 (14 requested) atoms. Cycle 22: After refmac, R = 0.1943 (Rfree = 0.000) for 5321 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 23: After refmac, R = 0.1934 (Rfree = 0.000) for 5311 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 24: After refmac, R = 0.1830 (Rfree = 0.000) for 5306 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 25: After refmac, R = 0.1393 (Rfree = 0.000) for 5298 atoms. Found 11 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5497 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5522 seeds are put forward Round 1: 262 peptides, 52 chains. Longest chain 12 peptides. Score 0.306 Round 2: 300 peptides, 53 chains. Longest chain 13 peptides. Score 0.384 Round 3: 322 peptides, 54 chains. Longest chain 13 peptides. Score 0.423 Round 4: 322 peptides, 51 chains. Longest chain 14 peptides. Score 0.450 Round 5: 330 peptides, 50 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 50, Residues 280, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12875 restraints for refining 5362 atoms. 11805 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2036 (Rfree = 0.000) for 5362 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 27: After refmac, R = 0.1926 (Rfree = 0.000) for 5320 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.1936 (Rfree = 0.000) for 5307 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 5294 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 5279 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 5478 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5497 seeds are put forward Round 1: 244 peptides, 52 chains. Longest chain 11 peptides. Score 0.261 Round 2: 282 peptides, 49 chains. Longest chain 17 peptides. Score 0.382 Round 3: 285 peptides, 50 chains. Longest chain 12 peptides. Score 0.379 Round 4: 284 peptides, 52 chains. Longest chain 10 peptides. Score 0.358 Round 5: 283 peptides, 47 chains. Longest chain 16 peptides. Score 0.404 Taking the results from Round 5 Chains 47, Residues 236, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12991 restraints for refining 5362 atoms. 12068 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1938 (Rfree = 0.000) for 5362 atoms. Found 22 (29 requested) and removed 79 (14 requested) atoms. Cycle 32: After refmac, R = 0.1778 (Rfree = 0.000) for 5284 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 33: After refmac, R = 0.1816 (Rfree = 0.000) for 5277 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.1823 (Rfree = 0.000) for 5265 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 35: After refmac, R = 0.1774 (Rfree = 0.000) for 5257 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5444 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5463 seeds are put forward Round 1: 223 peptides, 48 chains. Longest chain 8 peptides. Score 0.250 Round 2: 257 peptides, 50 chains. Longest chain 9 peptides. Score 0.314 Round 3: 267 peptides, 47 chains. Longest chain 10 peptides. Score 0.368 Round 4: 268 peptides, 48 chains. Longest chain 10 peptides. Score 0.360 Round 5: 279 peptides, 47 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 47, Residues 232, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 13005 restraints for refining 5362 atoms. 12124 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2014 (Rfree = 0.000) for 5362 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 37: After refmac, R = 0.2061 (Rfree = 0.000) for 5348 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 5336 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 39: After refmac, R = 0.1961 (Rfree = 0.000) for 5326 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 40: After refmac, R = 0.1795 (Rfree = 0.000) for 5315 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 5515 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5528 seeds are put forward Round 1: 192 peptides, 39 chains. Longest chain 10 peptides. Score 0.268 Round 2: 229 peptides, 43 chains. Longest chain 11 peptides. Score 0.319 Round 3: 240 peptides, 44 chains. Longest chain 13 peptides. Score 0.335 Round 4: 235 peptides, 40 chains. Longest chain 15 peptides. Score 0.364 Round 5: 241 peptides, 43 chains. Longest chain 13 peptides. Score 0.348 Taking the results from Round 4 Chains 40, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 13165 restraints for refining 5353 atoms. 12425 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1916 (Rfree = 0.000) for 5353 atoms. Found 29 (29 requested) and removed 44 (14 requested) atoms. Cycle 42: After refmac, R = 0.1716 (Rfree = 0.000) for 5330 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 43: After refmac, R = 0.1776 (Rfree = 0.000) for 5322 atoms. Found 29 (29 requested) and removed 36 (14 requested) atoms. Cycle 44: After refmac, R = 0.1650 (Rfree = 0.000) for 5308 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 45: After refmac, R = 0.1799 (Rfree = 0.000) for 5310 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5490 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5505 seeds are put forward Round 1: 187 peptides, 42 chains. Longest chain 7 peptides. Score 0.221 Round 2: 220 peptides, 39 chains. Longest chain 13 peptides. Score 0.339 Round 3: 224 peptides, 41 chains. Longest chain 9 peptides. Score 0.328 Round 4: 222 peptides, 38 chains. Longest chain 12 peptides. Score 0.354 Round 5: 239 peptides, 41 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 198, 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 1vr0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7656 reflections ( 99.57 % complete ) and 12846 restraints for refining 5333 atoms. 12095 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1967 (Rfree = 0.000) for 5333 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1964 (Rfree = 0.000) for 5285 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 5257 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1784 (Rfree = 0.000) for 5232 atoms. TimeTaking 57.98