null Mon 24 Dec 00:13:40 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 1vqr-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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/1vqr-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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 00:13:44 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/1vqr-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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 844 and 0 Target number of residues in the AU: 844 Target solvent content: 0.6358 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-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 69.50 11006 reflections ( 89.82 % complete ) and 0 restraints for refining 10563 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3726 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3416 (Rfree = 0.000) for 10563 atoms. Found 57 (58 requested) and removed 238 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 10500 seeds are put forward NCS extension: 0 residues added, 10500 seeds are put forward Round 1: 235 peptides, 55 chains. Longest chain 8 peptides. Score 0.194 Round 2: 297 peptides, 64 chains. Longest chain 9 peptides. Score 0.236 Round 3: 322 peptides, 68 chains. Longest chain 10 peptides. Score 0.250 Round 4: 346 peptides, 67 chains. Longest chain 12 peptides. Score 0.293 Round 5: 362 peptides, 70 chains. Longest chain 12 peptides. Score 0.298 Taking the results from Round 5 Chains 70, Residues 292, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21765 restraints for refining 8589 atoms. 20643 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 8589 atoms. Found 47 (47 requested) and removed 78 (23 requested) atoms. Cycle 2: After refmac, R = 0.2641 (Rfree = 0.000) for 8464 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 3: After refmac, R = 0.2118 (Rfree = 0.000) for 8407 atoms. Found 16 (46 requested) and removed 46 (23 requested) atoms. Cycle 4: After refmac, R = 0.2018 (Rfree = 0.000) for 8348 atoms. Found 16 (46 requested) and removed 39 (23 requested) atoms. Cycle 5: After refmac, R = 0.1952 (Rfree = 0.000) for 8311 atoms. Found 12 (45 requested) and removed 34 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 8482 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8495 seeds are put forward Round 1: 342 peptides, 69 chains. Longest chain 10 peptides. Score 0.274 Round 2: 362 peptides, 66 chains. Longest chain 12 peptides. Score 0.323 Round 3: 414 peptides, 77 chains. Longest chain 13 peptides. Score 0.329 Round 4: 431 peptides, 78 chains. Longest chain 12 peptides. Score 0.347 Round 5: 420 peptides, 73 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 5 Chains 73, Residues 347, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20141 restraints for refining 8220 atoms. 18826 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2403 (Rfree = 0.000) for 8220 atoms. Found 43 (45 requested) and removed 70 (22 requested) atoms. Cycle 7: After refmac, R = 0.2327 (Rfree = 0.000) for 8156 atoms. Found 32 (45 requested) and removed 59 (22 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 8092 atoms. Found 34 (44 requested) and removed 62 (22 requested) atoms. Cycle 9: After refmac, R = 0.2088 (Rfree = 0.000) for 8045 atoms. Found 32 (44 requested) and removed 39 (22 requested) atoms. Cycle 10: After refmac, R = 0.2110 (Rfree = 0.000) for 8009 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 8217 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8232 seeds are put forward Round 1: 369 peptides, 81 chains. Longest chain 7 peptides. Score 0.238 Round 2: 431 peptides, 80 chains. Longest chain 14 peptides. Score 0.335 Round 3: 430 peptides, 78 chains. Longest chain 11 peptides. Score 0.346 Round 4: 413 peptides, 74 chains. Longest chain 11 peptides. Score 0.346 Round 5: 395 peptides, 70 chains. Longest chain 13 peptides. Score 0.345 Taking the results from Round 4 Chains 74, Residues 339, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 19932 restraints for refining 8210 atoms. 18632 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2151 (Rfree = 0.000) for 8210 atoms. Found 22 (45 requested) and removed 73 (22 requested) atoms. Cycle 12: After refmac, R = 0.2206 (Rfree = 0.000) for 8127 atoms. Found 37 (44 requested) and removed 50 (22 requested) atoms. Cycle 13: After refmac, R = 0.2059 (Rfree = 0.000) for 8092 atoms. Found 28 (44 requested) and removed 40 (22 requested) atoms. Cycle 14: After refmac, R = 0.2031 (Rfree = 0.000) for 8051 atoms. Found 39 (44 requested) and removed 42 (22 requested) atoms. Cycle 15: After refmac, R = 0.1947 (Rfree = 0.000) for 8033 atoms. Found 29 (44 requested) and removed 37 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 8264 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8276 seeds are put forward Round 1: 369 peptides, 82 chains. Longest chain 9 peptides. Score 0.232 Round 2: 428 peptides, 84 chains. Longest chain 10 peptides. Score 0.307 Round 3: 421 peptides, 81 chains. Longest chain 11 peptides. Score 0.315 Round 4: 411 peptides, 75 chains. Longest chain 12 peptides. Score 0.337 Round 5: 428 peptides, 77 chains. Longest chain 15 peptides. Score 0.349 Taking the results from Round 5 Chains 77, Residues 351, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20269 restraints for refining 8360 atoms. 18942 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1999 (Rfree = 0.000) for 8360 atoms. Found 32 (45 requested) and removed 50 (22 requested) atoms. Cycle 17: After refmac, R = 0.2013 (Rfree = 0.000) for 8301 atoms. Found 33 (45 requested) and removed 37 (22 requested) atoms. Cycle 18: After refmac, R = 0.2140 (Rfree = 0.000) for 8278 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 8249 atoms. Found 35 (45 requested) and removed 40 (22 requested) atoms. Cycle 20: After refmac, R = 0.2162 (Rfree = 0.000) for 8223 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 8427 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8447 seeds are put forward Round 1: 367 peptides, 78 chains. Longest chain 9 peptides. Score 0.254 Round 2: 410 peptides, 78 chains. Longest chain 13 peptides. Score 0.318 Round 3: 414 peptides, 77 chains. Longest chain 11 peptides. Score 0.329 Round 4: 432 peptides, 76 chains. Longest chain 19 peptides. Score 0.360 Round 5: 418 peptides, 74 chains. Longest chain 20 peptides. Score 0.353 Taking the results from Round 4 Chains 77, Residues 356, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20368 restraints for refining 8461 atoms. 18954 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2161 (Rfree = 0.000) for 8461 atoms. Found 46 (46 requested) and removed 78 (23 requested) atoms. Cycle 22: After refmac, R = 0.2156 (Rfree = 0.000) for 8410 atoms. Found 46 (46 requested) and removed 50 (23 requested) atoms. Cycle 23: After refmac, R = 0.1743 (Rfree = 0.000) for 8384 atoms. Found 12 (46 requested) and removed 34 (23 requested) atoms. Cycle 24: After refmac, R = 0.1676 (Rfree = 0.000) for 8349 atoms. Found 7 (45 requested) and removed 28 (22 requested) atoms. Cycle 25: After refmac, R = 0.1626 (Rfree = 0.000) for 8321 atoms. Found 7 (45 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 8488 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8503 seeds are put forward Round 1: 382 peptides, 80 chains. Longest chain 11 peptides. Score 0.264 Round 2: 420 peptides, 78 chains. Longest chain 12 peptides. Score 0.332 Round 3: 428 peptides, 74 chains. Longest chain 13 peptides. Score 0.366 Round 4: 446 peptides, 79 chains. Longest chain 15 peptides. Score 0.361 Round 5: 439 peptides, 78 chains. Longest chain 15 peptides. Score 0.358 Taking the results from Round 3 Chains 74, Residues 354, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20799 restraints for refining 8542 atoms. 19457 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 8542 atoms. Found 46 (46 requested) and removed 56 (23 requested) atoms. Cycle 27: After refmac, R = 0.2144 (Rfree = 0.000) for 8501 atoms. Found 46 (46 requested) and removed 55 (23 requested) atoms. Cycle 28: After refmac, R = 0.2166 (Rfree = 0.000) for 8475 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 8453 atoms. Found 46 (46 requested) and removed 46 (23 requested) atoms. Cycle 30: After refmac, R = 0.1717 (Rfree = 0.000) for 8443 atoms. Found 9 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 8579 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8601 seeds are put forward Round 1: 343 peptides, 75 chains. Longest chain 9 peptides. Score 0.237 Round 2: 392 peptides, 77 chains. Longest chain 10 peptides. Score 0.298 Round 3: 425 peptides, 81 chains. Longest chain 13 peptides. Score 0.321 Round 4: 397 peptides, 75 chains. Longest chain 10 peptides. Score 0.317 Round 5: 417 peptides, 76 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 5 Chains 76, Residues 341, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21109 restraints for refining 8594 atoms. 19821 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2315 (Rfree = 0.000) for 8594 atoms. Found 47 (47 requested) and removed 80 (23 requested) atoms. Cycle 32: After refmac, R = 0.2190 (Rfree = 0.000) for 8536 atoms. Found 47 (47 requested) and removed 150 (23 requested) atoms. Cycle 33: After refmac, R = 0.2068 (Rfree = 0.000) for 8416 atoms. Found 46 (46 requested) and removed 53 (23 requested) atoms. Cycle 34: After refmac, R = 0.1755 (Rfree = 0.000) for 8387 atoms. Found 10 (46 requested) and removed 29 (23 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 8358 atoms. Found 8 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 8527 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8550 seeds are put forward Round 1: 331 peptides, 71 chains. Longest chain 9 peptides. Score 0.244 Round 2: 350 peptides, 67 chains. Longest chain 14 peptides. Score 0.299 Round 3: 361 peptides, 70 chains. Longest chain 9 peptides. Score 0.296 Round 4: 357 peptides, 65 chains. Longest chain 14 peptides. Score 0.322 Round 5: 351 peptides, 63 chains. Longest chain 15 peptides. Score 0.326 Taking the results from Round 5 Chains 63, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21402 restraints for refining 8589 atoms. 20313 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 8589 atoms. Found 47 (47 requested) and removed 61 (23 requested) atoms. Cycle 37: After refmac, R = 0.2186 (Rfree = 0.000) for 8551 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. Cycle 38: After refmac, R = 0.2094 (Rfree = 0.000) for 8537 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. Cycle 39: After refmac, R = 0.2080 (Rfree = 0.000) for 8520 atoms. Found 46 (46 requested) and removed 39 (23 requested) atoms. Cycle 40: After refmac, R = 0.1678 (Rfree = 0.000) for 8514 atoms. Found 6 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 8674 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8689 seeds are put forward Round 1: 265 peptides, 60 chains. Longest chain 8 peptides. Score 0.211 Round 2: 324 peptides, 66 chains. Longest chain 10 peptides. Score 0.266 Round 3: 322 peptides, 59 chains. Longest chain 15 peptides. Score 0.309 Round 4: 332 peptides, 64 chains. Longest chain 11 peptides. Score 0.291 Round 5: 331 peptides, 64 chains. Longest chain 12 peptides. Score 0.290 Taking the results from Round 3 Chains 59, Residues 263, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21015 restraints for refining 8432 atoms. 20022 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2126 (Rfree = 0.000) for 8432 atoms. Found 46 (46 requested) and removed 63 (23 requested) atoms. Cycle 42: After refmac, R = 0.2191 (Rfree = 0.000) for 8387 atoms. Found 46 (46 requested) and removed 45 (23 requested) atoms. Cycle 43: After refmac, R = 0.1717 (Rfree = 0.000) for 8363 atoms. Found 15 (46 requested) and removed 32 (23 requested) atoms. Cycle 44: After refmac, R = 0.1605 (Rfree = 0.000) for 8334 atoms. Found 10 (45 requested) and removed 26 (22 requested) atoms. Cycle 45: After refmac, R = 0.1635 (Rfree = 0.000) for 8311 atoms. Found 21 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 8438 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 8459 seeds are put forward Round 1: 271 peptides, 63 chains. Longest chain 8 peptides. Score 0.200 Round 2: 313 peptides, 62 chains. Longest chain 15 peptides. Score 0.275 Round 3: 316 peptides, 64 chains. Longest chain 9 peptides. Score 0.267 Round 4: 312 peptides, 63 chains. Longest chain 11 peptides. Score 0.267 Round 5: 303 peptides, 59 chains. Longest chain 11 peptides. Score 0.280 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 244, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11006 reflections ( 89.82 % complete ) and 20703 restraints for refining 8354 atoms. 19786 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2083 (Rfree = 0.000) for 8354 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 8315 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2161 (Rfree = 0.000) for 8281 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 8240 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:56:48 GMT 2018 Job finished. TimeTaking 103.14 Used memory is bytes: 24257568