Mon 24 Dec 07:36:55 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 1vr0-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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/1vr0-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 07:36:59 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/1vr0-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6343 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: 1vr0-3.6-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.65 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 3.600 Wilson plot Bfac: 68.71 9023 reflections ( 99.64 % complete ) and 0 restraints for refining 6525 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3254 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3122 (Rfree = 0.000) for 6525 atoms. Found 41 (41 requested) and removed 46 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 6670 seeds are put forward NCS extension: 0 residues added, 6670 seeds are put forward Round 1: 274 peptides, 58 chains. Longest chain 10 peptides. Score 0.274 Round 2: 378 peptides, 64 chains. Longest chain 12 peptides. Score 0.450 Round 3: 387 peptides, 62 chains. Longest chain 14 peptides. Score 0.485 Round 4: 405 peptides, 61 chains. Longest chain 16 peptides. Score 0.527 Round 5: 405 peptides, 54 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 5 Chains 54, Residues 351, Estimated correctness of the model 7.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12441 restraints for refining 5372 atoms. 11091 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2541 (Rfree = 0.000) for 5372 atoms. Found 20 (34 requested) and removed 32 (17 requested) atoms. Cycle 2: After refmac, R = 0.2384 (Rfree = 0.000) for 5263 atoms. Found 15 (34 requested) and removed 29 (17 requested) atoms. Cycle 3: After refmac, R = 0.2279 (Rfree = 0.000) for 5217 atoms. Found 16 (33 requested) and removed 30 (16 requested) atoms. Cycle 4: After refmac, R = 0.2173 (Rfree = 0.000) for 5184 atoms. Found 13 (33 requested) and removed 23 (16 requested) atoms. Cycle 5: After refmac, R = 0.1771 (Rfree = 0.000) for 5155 atoms. Found 3 (33 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5348 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5367 seeds are put forward Round 1: 333 peptides, 64 chains. Longest chain 13 peptides. Score 0.353 Round 2: 405 peptides, 65 chains. Longest chain 17 peptides. Score 0.494 Round 3: 391 peptides, 59 chains. Longest chain 18 peptides. Score 0.517 Round 4: 390 peptides, 56 chains. Longest chain 25 peptides. Score 0.539 Round 5: 401 peptides, 57 chains. Longest chain 21 peptides. Score 0.551 Taking the results from Round 5 Chains 58, Residues 344, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12023 restraints for refining 5245 atoms. 10668 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2275 (Rfree = 0.000) for 5245 atoms. Found 17 (33 requested) and removed 51 (16 requested) atoms. Cycle 7: After refmac, R = 0.2174 (Rfree = 0.000) for 5172 atoms. Found 7 (33 requested) and removed 39 (16 requested) atoms. Cycle 8: After refmac, R = 0.2097 (Rfree = 0.000) for 5122 atoms. Found 11 (32 requested) and removed 36 (16 requested) atoms. Cycle 9: After refmac, R = 0.2025 (Rfree = 0.000) for 5083 atoms. Found 7 (32 requested) and removed 33 (16 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2096 (Rfree = 0.000) for 5045 atoms. Found 16 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 5278 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5301 seeds are put forward Round 1: 332 peptides, 63 chains. Longest chain 17 peptides. Score 0.361 Round 2: 393 peptides, 55 chains. Longest chain 19 peptides. Score 0.552 Round 3: 398 peptides, 58 chains. Longest chain 23 peptides. Score 0.538 Round 4: 382 peptides, 52 chains. Longest chain 21 peptides. Score 0.556 Round 5: 372 peptides, 52 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 4 Chains 52, Residues 330, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12317 restraints for refining 5313 atoms. 11049 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 5313 atoms. Found 19 (34 requested) and removed 46 (17 requested) atoms. Cycle 12: After refmac, R = 0.2195 (Rfree = 0.000) for 5266 atoms. Found 17 (33 requested) and removed 40 (16 requested) atoms. Cycle 13: After refmac, R = 0.2140 (Rfree = 0.000) for 5231 atoms. Found 15 (33 requested) and removed 29 (16 requested) atoms. Cycle 14: After refmac, R = 0.2106 (Rfree = 0.000) for 5206 atoms. Found 15 (33 requested) and removed 23 (16 requested) atoms. Cycle 15: After refmac, R = 0.2079 (Rfree = 0.000) for 5189 atoms. Found 17 (33 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 5410 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5430 seeds are put forward Round 1: 316 peptides, 62 chains. Longest chain 12 peptides. Score 0.334 Round 2: 341 peptides, 52 chains. Longest chain 16 peptides. Score 0.480 Round 3: 355 peptides, 57 chains. Longest chain 14 peptides. Score 0.464 Round 4: 363 peptides, 53 chains. Longest chain 20 peptides. Score 0.514 Round 5: 343 peptides, 47 chains. Longest chain 22 peptides. Score 0.526 Taking the results from Round 5 Chains 47, Residues 296, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12542 restraints for refining 5373 atoms. 11391 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2290 (Rfree = 0.000) for 5373 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 17: After refmac, R = 0.2186 (Rfree = 0.000) for 5341 atoms. Found 32 (34 requested) and removed 26 (17 requested) atoms. Cycle 18: After refmac, R = 0.2125 (Rfree = 0.000) for 5325 atoms. Found 29 (34 requested) and removed 25 (17 requested) atoms. Cycle 19: After refmac, R = 0.2059 (Rfree = 0.000) for 5317 atoms. Found 33 (34 requested) and removed 29 (17 requested) atoms. Cycle 20: After refmac, R = 0.2019 (Rfree = 0.000) for 5308 atoms. Found 30 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 5550 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5562 seeds are put forward Round 1: 297 peptides, 59 chains. Longest chain 9 peptides. Score 0.319 Round 2: 340 peptides, 58 chains. Longest chain 15 peptides. Score 0.424 Round 3: 353 peptides, 59 chains. Longest chain 14 peptides. Score 0.442 Round 4: 355 peptides, 55 chains. Longest chain 16 peptides. Score 0.481 Round 5: 368 peptides, 59 chains. Longest chain 20 peptides. Score 0.473 Taking the results from Round 4 Chains 55, Residues 300, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12497 restraints for refining 5373 atoms. 11352 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2068 (Rfree = 0.000) for 5373 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 22: After refmac, R = 0.2117 (Rfree = 0.000) for 5350 atoms. Found 26 (34 requested) and removed 28 (17 requested) atoms. Cycle 23: After refmac, R = 0.1982 (Rfree = 0.000) for 5329 atoms. Found 22 (34 requested) and removed 24 (17 requested) atoms. Cycle 24: After refmac, R = 0.2104 (Rfree = 0.000) for 5314 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 25: After refmac, R = 0.2021 (Rfree = 0.000) for 5313 atoms. Found 28 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 5551 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5573 seeds are put forward Round 1: 281 peptides, 60 chains. Longest chain 10 peptides. Score 0.271 Round 2: 334 peptides, 55 chains. Longest chain 17 peptides. Score 0.439 Round 3: 311 peptides, 52 chains. Longest chain 18 peptides. Score 0.418 Round 4: 322 peptides, 50 chains. Longest chain 19 peptides. Score 0.459 Round 5: 330 peptides, 50 chains. Longest chain 18 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 ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12434 restraints for refining 5372 atoms. 11364 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2261 (Rfree = 0.000) for 5372 atoms. Found 29 (34 requested) and removed 30 (17 requested) atoms. Cycle 27: After refmac, R = 0.2225 (Rfree = 0.000) for 5340 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 28: After refmac, R = 0.2104 (Rfree = 0.000) for 5333 atoms. Found 25 (34 requested) and removed 31 (17 requested) atoms. Cycle 29: After refmac, R = 0.2019 (Rfree = 0.000) for 5315 atoms. Found 29 (34 requested) and removed 24 (17 requested) atoms. Cycle 30: After refmac, R = 0.2002 (Rfree = 0.000) for 5309 atoms. Found 23 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 5543 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5557 seeds are put forward Round 1: 276 peptides, 57 chains. Longest chain 11 peptides. Score 0.289 Round 2: 336 peptides, 60 chains. Longest chain 18 peptides. Score 0.397 Round 3: 314 peptides, 54 chains. Longest chain 15 peptides. Score 0.405 Round 4: 311 peptides, 53 chains. Longest chain 12 peptides. Score 0.408 Round 5: 316 peptides, 56 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 4 Chains 53, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12640 restraints for refining 5373 atoms. 11661 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2178 (Rfree = 0.000) for 5373 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 5351 atoms. Found 32 (34 requested) and removed 25 (17 requested) atoms. Cycle 33: After refmac, R = 0.1887 (Rfree = 0.000) for 5344 atoms. Found 28 (34 requested) and removed 29 (17 requested) atoms. Cycle 34: After refmac, R = 0.1775 (Rfree = 0.000) for 5335 atoms. Found 21 (34 requested) and removed 22 (17 requested) atoms. Cycle 35: After refmac, R = 0.1779 (Rfree = 0.000) for 5326 atoms. Found 22 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 5537 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5551 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 13 peptides. Score 0.287 Round 2: 291 peptides, 50 chains. Longest chain 16 peptides. Score 0.393 Round 3: 291 peptides, 46 chains. Longest chain 13 peptides. Score 0.431 Round 4: 312 peptides, 53 chains. Longest chain 15 peptides. Score 0.410 Round 5: 334 peptides, 52 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 53, Residues 282, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12286 restraints for refining 5373 atoms. 11164 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2013 (Rfree = 0.000) for 5373 atoms. Found 26 (34 requested) and removed 29 (17 requested) atoms. Cycle 37: After refmac, R = 0.1862 (Rfree = 0.000) for 5351 atoms. Found 23 (34 requested) and removed 23 (17 requested) atoms. Cycle 38: After refmac, R = 0.1766 (Rfree = 0.000) for 5342 atoms. Found 16 (34 requested) and removed 20 (17 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 5333 atoms. Found 22 (34 requested) and removed 23 (17 requested) atoms. Cycle 40: After refmac, R = 0.1679 (Rfree = 0.000) for 5326 atoms. Found 16 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 5508 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5523 seeds are put forward Round 1: 288 peptides, 56 chains. Longest chain 11 peptides. Score 0.328 Round 2: 319 peptides, 56 chains. Longest chain 16 peptides. Score 0.398 Round 3: 322 peptides, 56 chains. Longest chain 17 peptides. Score 0.404 Round 4: 321 peptides, 53 chains. Longest chain 14 peptides. Score 0.430 Round 5: 303 peptides, 50 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 4 Chains 53, Residues 268, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12554 restraints for refining 5372 atoms. 11524 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2033 (Rfree = 0.000) for 5372 atoms. Found 29 (34 requested) and removed 25 (17 requested) atoms. Cycle 42: After refmac, R = 0.1888 (Rfree = 0.000) for 5355 atoms. Found 26 (34 requested) and removed 23 (17 requested) atoms. Cycle 43: After refmac, R = 0.1788 (Rfree = 0.000) for 5350 atoms. Found 16 (34 requested) and removed 22 (17 requested) atoms. Cycle 44: After refmac, R = 0.1776 (Rfree = 0.000) for 5335 atoms. Found 24 (34 requested) and removed 21 (17 requested) atoms. Cycle 45: After refmac, R = 0.1760 (Rfree = 0.000) for 5333 atoms. Found 27 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 5546 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5559 seeds are put forward Round 1: 241 peptides, 50 chains. Longest chain 10 peptides. Score 0.275 Round 2: 265 peptides, 48 chains. Longest chain 9 peptides. Score 0.353 Round 3: 281 peptides, 53 chains. Longest chain 10 peptides. Score 0.341 Round 4: 286 peptides, 52 chains. Longest chain 11 peptides. Score 0.362 Round 5: 284 peptides, 50 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 234, 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. 9023 reflections ( 99.64 % complete ) and 12617 restraints for refining 5373 atoms. 11731 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1925 (Rfree = 0.000) for 5373 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1813 (Rfree = 0.000) for 5334 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1794 (Rfree = 0.000) for 5305 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1518 (Rfree = 0.000) for 5285 atoms. TimeTaking 58.43