null Mon 24 Dec 01:02:02 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 2gvh-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 01:02:07 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/2gvh-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 702 and 0 Target number of residues in the AU: 702 Target solvent content: 0.6840 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.90 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: 121.211 4.000 Wilson plot Bfac: 104.73 10161 reflections ( 99.57 % complete ) and 0 restraints for refining 7626 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3576 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3312 (Rfree = 0.000) for 7626 atoms. Found 36 (36 requested) and removed 117 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.94 3.39 Search for helices and strands: 0 residues in 0 chains, 7631 seeds are put forward NCS extension: 0 residues added, 7631 seeds are put forward Round 1: 351 peptides, 64 chains. Longest chain 14 peptides. Score 0.324 Round 2: 411 peptides, 68 chains. Longest chain 17 peptides. Score 0.386 Round 3: 417 peptides, 55 chains. Longest chain 19 peptides. Score 0.471 Round 4: 423 peptides, 61 chains. Longest chain 18 peptides. Score 0.444 Round 5: 429 peptides, 57 chains. Longest chain 23 peptides. Score 0.475 Taking the results from Round 5 Chains 59, Residues 372, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14839 restraints for refining 6239 atoms. 13313 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2596 (Rfree = 0.000) for 6239 atoms. Found 20 (29 requested) and removed 25 (14 requested) atoms. Cycle 2: After refmac, R = 0.2516 (Rfree = 0.000) for 6152 atoms. Found 9 (29 requested) and removed 22 (14 requested) atoms. Cycle 3: After refmac, R = 0.2465 (Rfree = 0.000) for 6109 atoms. Found 9 (29 requested) and removed 16 (14 requested) atoms. Cycle 4: After refmac, R = 0.2391 (Rfree = 0.000) for 6091 atoms. Found 3 (28 requested) and removed 20 (14 requested) atoms. Cycle 5: After refmac, R = 0.2368 (Rfree = 0.000) for 6069 atoms. Found 0 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 3.35 Search for helices and strands: 0 residues in 0 chains, 6210 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6235 seeds are put forward Round 1: 389 peptides, 68 chains. Longest chain 13 peptides. Score 0.354 Round 2: 407 peptides, 58 chains. Longest chain 27 peptides. Score 0.440 Round 3: 446 peptides, 64 chains. Longest chain 20 peptides. Score 0.456 Round 4: 454 peptides, 58 chains. Longest chain 24 peptides. Score 0.500 Round 5: 433 peptides, 60 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 4 Chains 66, Residues 396, Estimated correctness of the model 0.0 % 8 chains (77 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 13655 restraints for refining 6239 atoms. 11852 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2481 (Rfree = 0.000) for 6239 atoms. Found 16 (29 requested) and removed 33 (14 requested) atoms. Cycle 7: After refmac, R = 0.2402 (Rfree = 0.000) for 6171 atoms. Found 6 (29 requested) and removed 20 (14 requested) atoms. Cycle 8: After refmac, R = 0.2415 (Rfree = 0.000) for 6132 atoms. Found 7 (29 requested) and removed 20 (14 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 6106 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.2358 (Rfree = 0.000) for 6089 atoms. Found 2 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.90 3.36 Search for helices and strands: 0 residues in 0 chains, 6227 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6244 seeds are put forward Round 1: 411 peptides, 73 chains. Longest chain 14 peptides. Score 0.355 Round 2: 448 peptides, 68 chains. Longest chain 19 peptides. Score 0.435 Round 3: 444 peptides, 69 chains. Longest chain 15 peptides. Score 0.424 Round 4: 439 peptides, 67 chains. Longest chain 19 peptides. Score 0.429 Round 5: 450 peptides, 71 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 2 Chains 69, Residues 380, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14636 restraints for refining 6240 atoms. 13098 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2442 (Rfree = 0.000) for 6240 atoms. Found 19 (29 requested) and removed 23 (14 requested) atoms. Cycle 12: After refmac, R = 0.2388 (Rfree = 0.000) for 6198 atoms. Found 6 (29 requested) and removed 19 (14 requested) atoms. Cycle 13: After refmac, R = 0.2391 (Rfree = 0.000) for 6176 atoms. Found 1 (29 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.2371 (Rfree = 0.000) for 6157 atoms. Found 1 (29 requested) and removed 19 (14 requested) atoms. Cycle 15: After refmac, R = 0.2340 (Rfree = 0.000) for 6130 atoms. Found 1 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 3.39 Search for helices and strands: 0 residues in 0 chains, 6229 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6263 seeds are put forward Round 1: 389 peptides, 75 chains. Longest chain 12 peptides. Score 0.310 Round 2: 415 peptides, 66 chains. Longest chain 18 peptides. Score 0.403 Round 3: 429 peptides, 67 chains. Longest chain 14 peptides. Score 0.416 Round 4: 427 peptides, 62 chains. Longest chain 18 peptides. Score 0.443 Round 5: 456 peptides, 64 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 5 Chains 66, Residues 392, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14483 restraints for refining 6241 atoms. 12794 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2591 (Rfree = 0.000) for 6241 atoms. Found 23 (29 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.2447 (Rfree = 0.000) for 6207 atoms. Found 7 (29 requested) and removed 18 (14 requested) atoms. Cycle 18: After refmac, R = 0.2383 (Rfree = 0.000) for 6180 atoms. Found 10 (29 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.2365 (Rfree = 0.000) for 6167 atoms. Found 6 (29 requested) and removed 18 (14 requested) atoms. Cycle 20: After refmac, R = 0.2316 (Rfree = 0.000) for 6151 atoms. Found 2 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.95 3.40 Search for helices and strands: 0 residues in 0 chains, 6303 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6317 seeds are put forward Round 1: 356 peptides, 71 chains. Longest chain 11 peptides. Score 0.286 Round 2: 398 peptides, 66 chains. Longest chain 14 peptides. Score 0.380 Round 3: 391 peptides, 60 chains. Longest chain 20 peptides. Score 0.407 Round 4: 401 peptides, 61 chains. Longest chain 15 peptides. Score 0.414 Round 5: 411 peptides, 59 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 59, Residues 352, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 15151 restraints for refining 6238 atoms. 13751 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2377 (Rfree = 0.000) for 6238 atoms. Found 19 (29 requested) and removed 26 (14 requested) atoms. Cycle 22: After refmac, R = 0.2219 (Rfree = 0.000) for 6191 atoms. Found 3 (29 requested) and removed 17 (14 requested) atoms. Cycle 23: After refmac, R = 0.2168 (Rfree = 0.000) for 6167 atoms. Found 4 (29 requested) and removed 17 (14 requested) atoms. Cycle 24: After refmac, R = 0.2214 (Rfree = 0.000) for 6144 atoms. Found 4 (29 requested) and removed 16 (14 requested) atoms. Cycle 25: After refmac, R = 0.2185 (Rfree = 0.000) for 6130 atoms. Found 1 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.92 3.38 Search for helices and strands: 0 residues in 0 chains, 6275 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6290 seeds are put forward Round 1: 371 peptides, 73 chains. Longest chain 11 peptides. Score 0.296 Round 2: 394 peptides, 64 chains. Longest chain 20 peptides. Score 0.386 Round 3: 411 peptides, 67 chains. Longest chain 27 peptides. Score 0.392 Round 4: 429 peptides, 66 chains. Longest chain 15 peptides. Score 0.422 Round 5: 431 peptides, 65 chains. Longest chain 19 peptides. Score 0.431 Taking the results from Round 5 Chains 66, Residues 366, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14961 restraints for refining 6240 atoms. 13513 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2377 (Rfree = 0.000) for 6240 atoms. Found 20 (29 requested) and removed 47 (14 requested) atoms. Cycle 27: After refmac, R = 0.2150 (Rfree = 0.000) for 6165 atoms. Found 13 (29 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.2037 (Rfree = 0.000) for 6135 atoms. Found 0 (29 requested) and removed 29 (14 requested) atoms. Cycle 29: After refmac, R = 0.2020 (Rfree = 0.000) for 6100 atoms. Found 1 (29 requested) and removed 26 (14 requested) atoms. Cycle 30: After refmac, R = 0.2081 (Rfree = 0.000) for 6072 atoms. Found 7 (28 requested) and removed 32 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.90 3.36 Search for helices and strands: 0 residues in 0 chains, 6211 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6225 seeds are put forward Round 1: 331 peptides, 61 chains. Longest chain 14 peptides. Score 0.313 Round 2: 368 peptides, 59 chains. Longest chain 11 peptides. Score 0.381 Round 3: 389 peptides, 61 chains. Longest chain 16 peptides. Score 0.398 Round 4: 393 peptides, 57 chains. Longest chain 24 peptides. Score 0.428 Round 5: 400 peptides, 58 chains. Longest chain 21 peptides. Score 0.431 Taking the results from Round 5 Chains 60, Residues 342, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14603 restraints for refining 6242 atoms. 13198 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2404 (Rfree = 0.000) for 6242 atoms. Found 22 (29 requested) and removed 49 (14 requested) atoms. Cycle 32: After refmac, R = 0.2257 (Rfree = 0.000) for 6189 atoms. Found 23 (29 requested) and removed 36 (14 requested) atoms. Cycle 33: After refmac, R = 0.2257 (Rfree = 0.000) for 6156 atoms. Found 15 (29 requested) and removed 32 (14 requested) atoms. Cycle 34: After refmac, R = 0.2241 (Rfree = 0.000) for 6116 atoms. Found 21 (29 requested) and removed 38 (14 requested) atoms. Cycle 35: After refmac, R = 0.2094 (Rfree = 0.000) for 6083 atoms. Found 17 (28 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6218 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6233 seeds are put forward Round 1: 334 peptides, 68 chains. Longest chain 10 peptides. Score 0.271 Round 2: 363 peptides, 65 chains. Longest chain 14 peptides. Score 0.335 Round 3: 376 peptides, 63 chains. Longest chain 14 peptides. Score 0.367 Round 4: 356 peptides, 61 chains. Longest chain 12 peptides. Score 0.351 Round 5: 385 peptides, 61 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 61, Residues 324, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 14901 restraints for refining 6240 atoms. 13610 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2210 (Rfree = 0.000) for 6240 atoms. Found 22 (29 requested) and removed 23 (14 requested) atoms. Cycle 37: After refmac, R = 0.2271 (Rfree = 0.000) for 6187 atoms. Found 24 (29 requested) and removed 24 (14 requested) atoms. Cycle 38: After refmac, R = 0.2245 (Rfree = 0.000) for 6161 atoms. Found 26 (29 requested) and removed 27 (14 requested) atoms. Cycle 39: After refmac, R = 0.2156 (Rfree = 0.000) for 6135 atoms. Found 16 (29 requested) and removed 31 (14 requested) atoms. Cycle 40: After refmac, R = 0.2199 (Rfree = 0.000) for 6095 atoms. Found 27 (29 requested) and removed 29 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.33 Search for helices and strands: 0 residues in 0 chains, 6317 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6336 seeds are put forward Round 1: 286 peptides, 63 chains. Longest chain 7 peptides. Score 0.227 Round 2: 315 peptides, 59 chains. Longest chain 11 peptides. Score 0.302 Round 3: 336 peptides, 58 chains. Longest chain 13 peptides. Score 0.341 Round 4: 333 peptides, 55 chains. Longest chain 13 peptides. Score 0.356 Round 5: 318 peptides, 52 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 4 Chains 55, Residues 278, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10161 reflections ( 99.57 % complete ) and 15082 restraints for refining 6240 atoms. 13960 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2218 (Rfree = 0.000) for 6240 atoms. Found 21 (29 requested) and removed 27 (14 requested) atoms. Cycle 42: After refmac, R = 0.2302 (Rfree = 0.000) for 6206 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 43: After refmac, R = 0.2261 (Rfree = 0.000) for 6188 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 44: After refmac, R = 0.2215 (Rfree = 0.000) for 6167 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 45: After refmac, R = 0.2235 (Rfree = 0.000) for 6143 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.29 Search for helices and strands: 0 residues in 0 chains, 6310 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6324 seeds are put forward Round 1: 271 peptides, 57 chains. Longest chain 9 peptides. Score 0.244 Round 2: 305 peptides, 55 chains. Longest chain 12 peptides. Score 0.314 Round 3: 317 peptides, 53 chains. Longest chain 12 peptides. Score 0.346 Round 4: 313 peptides, 47 chains. Longest chain 22 peptides. Score 0.380 Round 5: 302 peptides, 51 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 266, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2gvh-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10161 reflections ( 99.57 % complete ) and 14924 restraints for refining 6242 atoms. 13885 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2347 (Rfree = 0.000) for 6242 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2258 (Rfree = 0.000) for 6190 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2364 (Rfree = 0.000) for 6155 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2184 (Rfree = 0.000) for 6116 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:19:28 GMT 2018 Job finished. TimeTaking 77.44 Used memory is bytes: 22687936