Mon 24 Dec 07:47:43 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 1vl5-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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/1vl5-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 07:47:48 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/1vl5-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 726 and 0 Target number of residues in the AU: 726 Target solvent content: 0.6608 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-4.0-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 4.000 Wilson plot Bfac: 85.29 9787 reflections ( 99.93 % complete ) and 0 restraints for refining 9214 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3436 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3201 (Rfree = 0.000) for 9214 atoms. Found 43 (43 requested) and removed 60 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 9357 seeds are put forward NCS extension: 0 residues added, 9357 seeds are put forward Round 1: 289 peptides, 62 chains. Longest chain 8 peptides. Score 0.241 Round 2: 384 peptides, 68 chains. Longest chain 14 peptides. Score 0.352 Round 3: 426 peptides, 69 chains. Longest chain 13 peptides. Score 0.406 Round 4: 468 peptides, 75 chains. Longest chain 18 peptides. Score 0.428 Round 5: 476 peptides, 71 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 71, Residues 405, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 18274 restraints for refining 7513 atoms. 16682 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2675 (Rfree = 0.000) for 7513 atoms. Found 17 (35 requested) and removed 66 (17 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2398 (Rfree = 0.000) for 7298 atoms. Found 28 (35 requested) and removed 46 (17 requested) atoms. Cycle 3: After refmac, R = 0.2019 (Rfree = 0.000) for 7176 atoms. Found 11 (34 requested) and removed 37 (17 requested) atoms. Cycle 4: After refmac, R = 0.2200 (Rfree = 0.000) for 7101 atoms. Found 21 (33 requested) and removed 38 (16 requested) atoms. Cycle 5: After refmac, R = 0.2230 (Rfree = 0.000) for 7042 atoms. Found 33 (33 requested) and removed 41 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7283 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7300 seeds are put forward Round 1: 394 peptides, 78 chains. Longest chain 11 peptides. Score 0.302 Round 2: 465 peptides, 73 chains. Longest chain 17 peptides. Score 0.436 Round 3: 475 peptides, 71 chains. Longest chain 19 peptides. Score 0.461 Round 4: 470 peptides, 70 chains. Longest chain 21 peptides. Score 0.460 Round 5: 482 peptides, 74 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 3 Chains 72, Residues 404, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 15922 restraints for refining 6996 atoms. 14301 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2251 (Rfree = 0.000) for 6996 atoms. Found 29 (33 requested) and removed 69 (16 requested) atoms. Cycle 7: After refmac, R = 0.2050 (Rfree = 0.000) for 6894 atoms. Found 29 (33 requested) and removed 38 (16 requested) atoms. Cycle 8: After refmac, R = 0.1939 (Rfree = 0.000) for 6849 atoms. Found 17 (32 requested) and removed 34 (16 requested) atoms. Cycle 9: After refmac, R = 0.1925 (Rfree = 0.000) for 6799 atoms. Found 26 (32 requested) and removed 41 (16 requested) atoms. Cycle 10: After refmac, R = 0.1872 (Rfree = 0.000) for 6764 atoms. Found 21 (32 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 6995 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 7019 seeds are put forward Round 1: 409 peptides, 78 chains. Longest chain 13 peptides. Score 0.325 Round 2: 455 peptides, 75 chains. Longest chain 14 peptides. Score 0.410 Round 3: 465 peptides, 64 chains. Longest chain 23 peptides. Score 0.488 Round 4: 468 peptides, 67 chains. Longest chain 27 peptides. Score 0.475 Round 5: 462 peptides, 66 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 3 Chains 64, Residues 401, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16477 restraints for refining 7163 atoms. 14900 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2258 (Rfree = 0.000) for 7163 atoms. Found 34 (34 requested) and removed 75 (17 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 7069 atoms. Found 24 (33 requested) and removed 46 (16 requested) atoms. Cycle 13: After refmac, R = 0.2159 (Rfree = 0.000) for 7022 atoms. Found 18 (33 requested) and removed 54 (16 requested) atoms. Cycle 14: After refmac, R = 0.2064 (Rfree = 0.000) for 6968 atoms. Found 20 (33 requested) and removed 39 (16 requested) atoms. Cycle 15: After refmac, R = 0.1646 (Rfree = 0.000) for 6932 atoms. Found 1 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7133 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7158 seeds are put forward Round 1: 414 peptides, 77 chains. Longest chain 12 peptides. Score 0.339 Round 2: 453 peptides, 71 chains. Longest chain 20 peptides. Score 0.431 Round 3: 452 peptides, 70 chains. Longest chain 16 peptides. Score 0.436 Round 4: 465 peptides, 73 chains. Longest chain 17 peptides. Score 0.436 Round 5: 470 peptides, 68 chains. Longest chain 18 peptides. Score 0.472 Taking the results from Round 5 Chains 68, Residues 402, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17338 restraints for refining 7383 atoms. 15798 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2352 (Rfree = 0.000) for 7383 atoms. Found 35 (35 requested) and removed 61 (17 requested) atoms. Cycle 17: After refmac, R = 0.2119 (Rfree = 0.000) for 7292 atoms. Found 25 (34 requested) and removed 54 (17 requested) atoms. Cycle 18: After refmac, R = 0.2079 (Rfree = 0.000) for 7211 atoms. Found 32 (34 requested) and removed 45 (17 requested) atoms. Cycle 19: After refmac, R = 0.2145 (Rfree = 0.000) for 7166 atoms. Found 33 (34 requested) and removed 43 (17 requested) atoms. Cycle 20: After refmac, R = 0.2029 (Rfree = 0.000) for 7132 atoms. Found 26 (34 requested) and removed 46 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7344 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7358 seeds are put forward Round 1: 348 peptides, 70 chains. Longest chain 9 peptides. Score 0.283 Round 2: 411 peptides, 70 chains. Longest chain 13 peptides. Score 0.379 Round 3: 418 peptides, 70 chains. Longest chain 14 peptides. Score 0.389 Round 4: 414 peptides, 68 chains. Longest chain 15 peptides. Score 0.396 Round 5: 439 peptides, 67 chains. Longest chain 17 peptides. Score 0.436 Taking the results from Round 5 Chains 67, Residues 372, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17280 restraints for refining 7396 atoms. 15832 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2180 (Rfree = 0.000) for 7396 atoms. Found 35 (35 requested) and removed 73 (17 requested) atoms. Cycle 22: After refmac, R = 0.2159 (Rfree = 0.000) for 7285 atoms. Found 34 (34 requested) and removed 51 (17 requested) atoms. Cycle 23: After refmac, R = 0.2077 (Rfree = 0.000) for 7238 atoms. Found 21 (34 requested) and removed 49 (17 requested) atoms. Cycle 24: After refmac, R = 0.2042 (Rfree = 0.000) for 7197 atoms. Found 27 (34 requested) and removed 35 (17 requested) atoms. Cycle 25: After refmac, R = 0.1921 (Rfree = 0.000) for 7166 atoms. Found 27 (34 requested) and removed 35 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 7419 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 7445 seeds are put forward Round 1: 345 peptides, 71 chains. Longest chain 11 peptides. Score 0.271 Round 2: 413 peptides, 75 chains. Longest chain 14 peptides. Score 0.350 Round 3: 423 peptides, 70 chains. Longest chain 16 peptides. Score 0.396 Round 4: 435 peptides, 71 chains. Longest chain 18 peptides. Score 0.407 Round 5: 441 peptides, 72 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 5 Chains 72, Residues 369, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17870 restraints for refining 7513 atoms. 16460 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2251 (Rfree = 0.000) for 7513 atoms. Found 34 (35 requested) and removed 59 (17 requested) atoms. Cycle 27: After refmac, R = 0.2006 (Rfree = 0.000) for 7426 atoms. Found 22 (35 requested) and removed 40 (17 requested) atoms. Cycle 28: After refmac, R = 0.2048 (Rfree = 0.000) for 7363 atoms. Found 21 (35 requested) and removed 41 (17 requested) atoms. Cycle 29: After refmac, R = 0.1568 (Rfree = 0.000) for 7305 atoms. Found 8 (34 requested) and removed 31 (17 requested) atoms. Cycle 30: After refmac, R = 0.1495 (Rfree = 0.000) for 7267 atoms. Found 11 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 7480 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7493 seeds are put forward Round 1: 306 peptides, 67 chains. Longest chain 7 peptides. Score 0.234 Round 2: 379 peptides, 69 chains. Longest chain 12 peptides. Score 0.338 Round 3: 396 peptides, 72 chains. Longest chain 12 peptides. Score 0.344 Round 4: 402 peptides, 69 chains. Longest chain 15 peptides. Score 0.372 Round 5: 400 peptides, 67 chains. Longest chain 18 peptides. Score 0.382 Taking the results from Round 5 Chains 68, Residues 333, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17575 restraints for refining 7433 atoms. 16283 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2109 (Rfree = 0.000) for 7433 atoms. Found 35 (35 requested) and removed 55 (17 requested) atoms. Cycle 32: After refmac, R = 0.2064 (Rfree = 0.000) for 7349 atoms. Found 35 (35 requested) and removed 47 (17 requested) atoms. Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 7300 atoms. Found 19 (34 requested) and removed 31 (17 requested) atoms. Cycle 34: After refmac, R = 0.1936 (Rfree = 0.000) for 7266 atoms. Found 30 (34 requested) and removed 23 (17 requested) atoms. Cycle 35: After refmac, R = 0.1452 (Rfree = 0.000) for 7254 atoms. Found 5 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7501 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7518 seeds are put forward Round 1: 297 peptides, 60 chains. Longest chain 13 peptides. Score 0.269 Round 2: 356 peptides, 66 chains. Longest chain 12 peptides. Score 0.323 Round 3: 366 peptides, 59 chains. Longest chain 17 peptides. Score 0.384 Round 4: 362 peptides, 61 chains. Longest chain 17 peptides. Score 0.365 Round 5: 340 peptides, 55 chains. Longest chain 21 peptides. Score 0.372 Taking the results from Round 3 Chains 59, Residues 307, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17040 restraints for refining 7287 atoms. 15871 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1927 (Rfree = 0.000) for 7287 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. Cycle 37: After refmac, R = 0.2070 (Rfree = 0.000) for 7251 atoms. Found 34 (34 requested) and removed 51 (17 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1865 (Rfree = 0.000) for 7209 atoms. Found 32 (34 requested) and removed 38 (17 requested) atoms. Cycle 39: After refmac, R = 0.1886 (Rfree = 0.000) for 7183 atoms. Found 22 (34 requested) and removed 28 (17 requested) atoms. Cycle 40: After refmac, R = 0.1828 (Rfree = 0.000) for 7159 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 7381 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7398 seeds are put forward Round 1: 286 peptides, 60 chains. Longest chain 10 peptides. Score 0.250 Round 2: 358 peptides, 68 chains. Longest chain 12 peptides. Score 0.312 Round 3: 347 peptides, 61 chains. Longest chain 14 peptides. Score 0.342 Round 4: 338 peptides, 59 chains. Longest chain 12 peptides. Score 0.342 Round 5: 340 peptides, 57 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 5 Chains 57, Residues 283, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17299 restraints for refining 7383 atoms. 16167 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2108 (Rfree = 0.000) for 7383 atoms. Found 35 (35 requested) and removed 55 (17 requested) atoms. Cycle 42: After refmac, R = 0.1886 (Rfree = 0.000) for 7322 atoms. Found 28 (34 requested) and removed 38 (17 requested) atoms. Cycle 43: After refmac, R = 0.1490 (Rfree = 0.000) for 7288 atoms. Found 10 (34 requested) and removed 23 (17 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 44: After refmac, R = 0.1365 (Rfree = 0.000) for 7250 atoms. Found 4 (34 requested) and removed 26 (17 requested) atoms. Cycle 45: After refmac, R = 0.1379 (Rfree = 0.000) for 7224 atoms. Found 5 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 7430 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7447 seeds are put forward Round 1: 269 peptides, 60 chains. Longest chain 9 peptides. Score 0.221 Round 2: 337 peptides, 64 chains. Longest chain 12 peptides. Score 0.306 Round 3: 342 peptides, 62 chains. Longest chain 12 peptides. Score 0.328 Round 4: 347 peptides, 64 chains. Longest chain 11 peptides. Score 0.322 Round 5: 347 peptides, 61 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 286, 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 1vl5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9787 reflections ( 99.93 % complete ) and 17522 restraints for refining 7409 atoms. 16439 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2242 (Rfree = 0.000) for 7409 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2086 (Rfree = 0.000) for 7348 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 7306 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1588 (Rfree = 0.000) for 7280 atoms. TimeTaking 78.38