Mon 24 Dec 07:30:23 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 1vp4-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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/1vp4-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 07:30:28 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/1vp4-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 700 and 0 Target number of residues in the AU: 700 Target solvent content: 0.6481 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.4-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.400 Wilson plot Bfac: 76.86 14842 reflections ( 99.78 % complete ) and 0 restraints for refining 7556 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3660 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3521 (Rfree = 0.000) for 7556 atoms. Found 57 (57 requested) and removed 195 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 7478 seeds are put forward NCS extension: 0 residues added, 7478 seeds are put forward Round 1: 340 peptides, 74 chains. Longest chain 11 peptides. Score 0.247 Round 2: 389 peptides, 72 chains. Longest chain 13 peptides. Score 0.343 Round 3: 428 peptides, 76 chains. Longest chain 11 peptides. Score 0.377 Round 4: 439 peptides, 78 chains. Longest chain 12 peptides. Score 0.380 Round 5: 442 peptides, 77 chains. Longest chain 15 peptides. Score 0.392 Taking the results from Round 5 Chains 77, Residues 365, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14077 restraints for refining 6183 atoms. 12652 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2986 (Rfree = 0.000) for 6183 atoms. Found 46 (46 requested) and removed 59 (23 requested) atoms. Cycle 2: After refmac, R = 0.2787 (Rfree = 0.000) for 6110 atoms. Found 36 (46 requested) and removed 39 (23 requested) atoms. Cycle 3: After refmac, R = 0.2650 (Rfree = 0.000) for 6081 atoms. Found 33 (46 requested) and removed 31 (23 requested) atoms. Cycle 4: After refmac, R = 0.2629 (Rfree = 0.000) for 6073 atoms. Found 29 (45 requested) and removed 35 (22 requested) atoms. Cycle 5: After refmac, R = 0.2389 (Rfree = 0.000) for 6052 atoms. Found 9 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 6320 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6333 seeds are put forward Round 1: 397 peptides, 76 chains. Longest chain 11 peptides. Score 0.328 Round 2: 460 peptides, 76 chains. Longest chain 13 peptides. Score 0.425 Round 3: 445 peptides, 72 chains. Longest chain 12 peptides. Score 0.428 Round 4: 464 peptides, 78 chains. Longest chain 14 peptides. Score 0.418 Round 5: 449 peptides, 68 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 5 Chains 70, Residues 381, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14108 restraints for refining 6183 atoms. 12577 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2523 (Rfree = 0.000) for 6183 atoms. Found 26 (46 requested) and removed 38 (23 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 6138 atoms. Found 13 (46 requested) and removed 27 (23 requested) atoms. Cycle 8: After refmac, R = 0.2370 (Rfree = 0.000) for 6101 atoms. Found 20 (46 requested) and removed 32 (23 requested) atoms. Cycle 9: After refmac, R = 0.2349 (Rfree = 0.000) for 6073 atoms. Found 22 (45 requested) and removed 27 (22 requested) atoms. Cycle 10: After refmac, R = 0.2158 (Rfree = 0.000) for 6055 atoms. Found 4 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 6303 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6322 seeds are put forward Round 1: 386 peptides, 72 chains. Longest chain 13 peptides. Score 0.338 Round 2: 452 peptides, 68 chains. Longest chain 17 peptides. Score 0.463 Round 3: 459 peptides, 67 chains. Longest chain 19 peptides. Score 0.479 Round 4: 474 peptides, 71 chains. Longest chain 19 peptides. Score 0.475 Round 5: 466 peptides, 68 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 5 Chains 70, Residues 398, Estimated correctness of the model 0.0 % 8 chains (52 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13669 restraints for refining 6182 atoms. 11998 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2668 (Rfree = 0.000) for 6182 atoms. Found 39 (46 requested) and removed 31 (23 requested) atoms. Cycle 12: After refmac, R = 0.2480 (Rfree = 0.000) for 6157 atoms. Found 35 (46 requested) and removed 33 (23 requested) atoms. Cycle 13: After refmac, R = 0.2493 (Rfree = 0.000) for 6139 atoms. Found 28 (46 requested) and removed 29 (23 requested) atoms. Cycle 14: After refmac, R = 0.2350 (Rfree = 0.000) for 6119 atoms. Found 23 (46 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.2217 (Rfree = 0.000) for 6099 atoms. Found 8 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 6317 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6332 seeds are put forward Round 1: 400 peptides, 73 chains. Longest chain 11 peptides. Score 0.353 Round 2: 461 peptides, 71 chains. Longest chain 17 peptides. Score 0.457 Round 3: 452 peptides, 68 chains. Longest chain 16 peptides. Score 0.463 Round 4: 445 peptides, 66 chains. Longest chain 24 peptides. Score 0.466 Round 5: 420 peptides, 62 chains. Longest chain 20 peptides. Score 0.455 Taking the results from Round 4 Chains 66, Residues 379, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14206 restraints for refining 6181 atoms. 12736 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2490 (Rfree = 0.000) for 6181 atoms. Found 41 (46 requested) and removed 37 (23 requested) atoms. Cycle 17: After refmac, R = 0.2404 (Rfree = 0.000) for 6152 atoms. Found 39 (46 requested) and removed 27 (23 requested) atoms. Cycle 18: After refmac, R = 0.2329 (Rfree = 0.000) for 6147 atoms. Found 24 (46 requested) and removed 36 (23 requested) atoms. Cycle 19: After refmac, R = 0.2209 (Rfree = 0.000) for 6122 atoms. Found 20 (46 requested) and removed 29 (23 requested) atoms. Cycle 20: After refmac, R = 0.2187 (Rfree = 0.000) for 6102 atoms. Found 14 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 6359 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 6391 seeds are put forward Round 1: 396 peptides, 78 chains. Longest chain 11 peptides. Score 0.313 Round 2: 436 peptides, 73 chains. Longest chain 14 peptides. Score 0.408 Round 3: 439 peptides, 70 chains. Longest chain 18 peptides. Score 0.432 Round 4: 439 peptides, 64 chains. Longest chain 18 peptides. Score 0.470 Round 5: 441 peptides, 67 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 4 Chains 65, Residues 375, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13793 restraints for refining 6183 atoms. 12229 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2466 (Rfree = 0.000) for 6183 atoms. Found 38 (46 requested) and removed 30 (23 requested) atoms. Cycle 22: After refmac, R = 0.2428 (Rfree = 0.000) for 6159 atoms. Found 36 (46 requested) and removed 29 (23 requested) atoms. Cycle 23: After refmac, R = 0.2358 (Rfree = 0.000) for 6154 atoms. Found 26 (46 requested) and removed 26 (23 requested) atoms. Cycle 24: After refmac, R = 0.2358 (Rfree = 0.000) for 6138 atoms. Found 16 (46 requested) and removed 25 (23 requested) atoms. Cycle 25: After refmac, R = 0.2215 (Rfree = 0.000) for 6125 atoms. Found 13 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 6339 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6365 seeds are put forward Round 1: 363 peptides, 72 chains. Longest chain 10 peptides. Score 0.300 Round 2: 406 peptides, 72 chains. Longest chain 12 peptides. Score 0.369 Round 3: 416 peptides, 66 chains. Longest chain 23 peptides. Score 0.424 Round 4: 417 peptides, 65 chains. Longest chain 22 peptides. Score 0.432 Round 5: 429 peptides, 69 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 65, Residues 352, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13881 restraints for refining 6183 atoms. 12438 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2372 (Rfree = 0.000) for 6183 atoms. Found 46 (46 requested) and removed 25 (23 requested) atoms. Cycle 27: After refmac, R = 0.2256 (Rfree = 0.000) for 6177 atoms. Found 23 (46 requested) and removed 27 (23 requested) atoms. Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 6163 atoms. Found 27 (46 requested) and removed 24 (23 requested) atoms. Cycle 29: After refmac, R = 0.2305 (Rfree = 0.000) for 6149 atoms. Found 43 (46 requested) and removed 23 (23 requested) atoms. Cycle 30: After refmac, R = 0.2140 (Rfree = 0.000) for 6153 atoms. Found 22 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6370 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6387 seeds are put forward Round 1: 362 peptides, 70 chains. Longest chain 12 peptides. Score 0.313 Round 2: 413 peptides, 71 chains. Longest chain 15 peptides. Score 0.387 Round 3: 418 peptides, 69 chains. Longest chain 14 peptides. Score 0.408 Round 4: 427 peptides, 67 chains. Longest chain 19 peptides. Score 0.434 Round 5: 431 peptides, 67 chains. Longest chain 17 peptides. Score 0.439 Taking the results from Round 5 Chains 67, Residues 364, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14233 restraints for refining 6183 atoms. 12829 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2327 (Rfree = 0.000) for 6183 atoms. Found 37 (46 requested) and removed 31 (23 requested) atoms. Cycle 32: After refmac, R = 0.2276 (Rfree = 0.000) for 6161 atoms. Found 31 (46 requested) and removed 26 (23 requested) atoms. Cycle 33: After refmac, R = 0.2069 (Rfree = 0.000) for 6152 atoms. Found 18 (46 requested) and removed 26 (23 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 6136 atoms. Found 18 (46 requested) and removed 26 (23 requested) atoms. Cycle 35: After refmac, R = 0.2206 (Rfree = 0.000) for 6118 atoms. Found 22 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6343 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6363 seeds are put forward Round 1: 344 peptides, 69 chains. Longest chain 11 peptides. Score 0.290 Round 2: 370 peptides, 58 chains. Longest chain 15 peptides. Score 0.408 Round 3: 384 peptides, 63 chains. Longest chain 15 peptides. Score 0.396 Round 4: 398 peptides, 61 chains. Longest chain 18 peptides. Score 0.430 Round 5: 403 peptides, 67 chains. Longest chain 23 peptides. Score 0.398 Taking the results from Round 4 Chains 61, Residues 337, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14346 restraints for refining 6181 atoms. 13059 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2360 (Rfree = 0.000) for 6181 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. Cycle 37: After refmac, R = 0.2243 (Rfree = 0.000) for 6174 atoms. Found 17 (46 requested) and removed 23 (23 requested) atoms. Cycle 38: After refmac, R = 0.2253 (Rfree = 0.000) for 6159 atoms. Found 18 (46 requested) and removed 24 (23 requested) atoms. Cycle 39: After refmac, R = 0.2274 (Rfree = 0.000) for 6144 atoms. Found 27 (46 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.2292 (Rfree = 0.000) for 6138 atoms. Found 28 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 6391 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6408 seeds are put forward Round 1: 326 peptides, 69 chains. Longest chain 8 peptides. Score 0.259 Round 2: 382 peptides, 64 chains. Longest chain 10 peptides. Score 0.386 Round 3: 398 peptides, 68 chains. Longest chain 11 peptides. Score 0.384 Round 4: 385 peptides, 64 chains. Longest chain 15 peptides. Score 0.391 Round 5: 403 peptides, 62 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 5 Chains 62, Residues 341, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14417 restraints for refining 6182 atoms. 13115 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2343 (Rfree = 0.000) for 6182 atoms. Found 32 (46 requested) and removed 26 (23 requested) atoms. Cycle 42: After refmac, R = 0.2363 (Rfree = 0.000) for 6172 atoms. Found 21 (46 requested) and removed 29 (23 requested) atoms. Cycle 43: After refmac, R = 0.2317 (Rfree = 0.000) for 6154 atoms. Found 36 (46 requested) and removed 27 (23 requested) atoms. Cycle 44: After refmac, R = 0.2268 (Rfree = 0.000) for 6150 atoms. Found 42 (46 requested) and removed 28 (23 requested) atoms. Cycle 45: After refmac, R = 0.2154 (Rfree = 0.000) for 6158 atoms. Found 21 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6360 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6376 seeds are put forward Round 1: 334 peptides, 71 chains. Longest chain 9 peptides. Score 0.258 Round 2: 367 peptides, 62 chains. Longest chain 12 peptides. Score 0.376 Round 3: 368 peptides, 57 chains. Longest chain 16 peptides. Score 0.412 Round 4: 375 peptides, 58 chains. Longest chain 17 peptides. Score 0.416 Round 5: 385 peptides, 58 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 327, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14842 reflections ( 99.78 % complete ) and 14417 restraints for refining 6183 atoms. 13152 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2256 (Rfree = 0.000) for 6183 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2186 (Rfree = 0.000) for 6145 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.2128 (Rfree = 0.000) for 6109 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2181 (Rfree = 0.000) for 6075 atoms. TimeTaking 66.22